Treatment of sirtuin (sirt) related diseases by inhibition of natural antisense transcript to a sirtuin (sirt)

ABSTRACT

The present invention relates to antisense oligonucleotide that modulate the expression of and/or function of a Sirtuin (SIRT), in particular, by targeting natural antisense polynucleotides of a Sirtuin (SIRT). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Sirtuins (SIRT)s.

FIELD OF THE INVENTION

The present application claims the priority of U.S. provisional patentapplication No. 61/330,427 filed May 3, 2010, U.S. provisional patentapplication No. 61/409,136 filed Nov 2, 2010, U.S. provisional patentapplication No. 61/412,066 filed Nov. 10, 2010 and U.S. provisionalpatent application No. 61/415,891 filed Nov. 22, 2010.

Embodiments of the invention comprise oligonucleotides modulatingexpression and/or function of a Sirtuin (SIRT) and associated molecules.

BACKGROUND

DNA-RNA and RNA-RNA hybridization are important to many aspects ofnucleic acid function including DNA replication, transcription, andtranslation. Hybridization is also central to a variety of technologiesthat either detect a particular nucleic acid or alter its expression.Antisense nucleotides, for example, disrupt gene expression byhybridizing to target RNA, thereby interfering with RNA splicing,transcription, translation, and replication. Antisense DNA has the addedfeature that DNA-RNA hybrids serve as a substrate for digestion byribonuclease H, an activity that is present in most cell types.Antisense molecules can be delivered into cells, as is the case foroligodeoxynucleotides (ODNs), or they can be expressed from endogenousgenes as RNA molecules. The FDA recently approved an antisense drug,VITRAVENE™ (for treatment of cytomegalovirus retinitis), reflecting thatantisense has therapeutic utility.

SUMMARY

In one embodiment, the invention provides methods for inhibiting theaction of a natural antisense transcript by using antisenseoligonucleotide(s) targeted to any region of the natural antisensetranscript resulting in up-regulation of the corresponding sense gene.It is also contemplated herein that inhibition of the natural antisensetranscript can be achieved by siRNA, ribozymes and small molecules,which are considered to be within the scope of the present invention.

One embodiment provides a method of modulating function and/orexpression of a Sirtuin (SIRT) polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to a reversecomplement of a polynucleotide comprising 5 to 30 consecutivenucleotides within nucleotides 1 to 1028 of SEQ ID NO: 9 or nucleotides1 to 429 of SEQ ID NO: 10, or nucleotides 1 to 508 of SEQ ID NO: 11 ornucleotides 1 to 593 of SEQ ID NO: 12, 1 to 373 of SEQ ID NO: 13, 1 to1713 of SEQ ID NO: 14, 1 to 660 of SEQ ID NO: 15, 1 to 589 of SEQ ID NO:16, 1 to 726 of SEQ ID NO: 17, 1 to 320 of SEQ ID NO: 18, 1 to 616 ofSEQ ID NO: 19, 1 to 492 of SEQ ID NO: 20, 1 to 428 of SEQ ID NO: 21, 1to 4041 of SEQ ID NO: 22 or 1 to 705 of SEQ ID NO: 23 or 1 to 2714 ofSEQ ID NO: 141 or 1 to 1757 of SEQ ID NO: 142 or 1 to 3647 of SEQ ID NO:143, thereby modulating function and/or expression of the Sirtuin (SIRT)polynucleotide in patient cells or tissues in vivo or in vitro.

In another embodiment, an oligonucleotide targets a natural antisensesequence of a Sirtuin (SIRT) polynucleotide, for example, nucleotidesset forth in SEQ ID NO: 9 to 23, 141 to 143, and any variants, alleles,homology, mutants, derivatives, fragments and complementary sequencesthereto. Examples of antisense oligonucleotides useful in practicing themethods of the present invention are set forth as SEQ ID NOS: 24 to 127.

Another embodiment provides a method of modulating function and/orexpression of a Sirtuin (SIRT) polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to a reversecomplement of an antisense of the Sirtuin (SIRT) polynucleotide; therebymodulating function and/or expression of the Sirtuin (SIRT)polynucleotide in patient cells or tissues is vivo or in vitro.

Another embodiment provides a method of modulating function and/orexpression of a Sirtuin (SIRT) polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to an antisenseoligonucleotide to a Sirtuin (SIRT) antisense polynucleotide; therebymodulating function and/or expression of the Sirtuin (SIRT)polynucleotide in patient cells or tissues in vivo or in vitro.

In one embodiment, a composition comprises one or more antisenseoligonucleotides which bind to sense and/or antisense Sirtuin (SIRT)polynucleotides.

In another embodiment, the oligonucleotides comprise one or moremodified or substituted nucleotides.

In another embodiment, the oligonucleotides comprise one or moremodified bonds.

In yet another embodiment, the modified nucleotides comprise modifiedbases comprising phosphorothioate, methylphosphonate, peptide nucleicacids, 2′-O-methyl, flouro- or carbon, methylene or other locked nucleicacid (LNA) molecules. Preferably, the modified nucleotides are lockednucleic acid molecules, including α-L-LNA.

In another embodiment, the oligonucleotides are administered to apatient subcutaneously, intramuscularly, intravenously orintraperitoneally.

In another embodiment, the oligonucleotides are administered in apharmaceutical composition. A treatment regimen comprises administeringthe antisense compounds at least once to patient; however, thistreatment can be modified to include multiple doses over a period oftime. The treatment can be combined with one or more other types oftherapies.

In another embodiment, the oligonucleotides are encapsulated in aliposome or attached to a carrier molecule (e.g. cholesterol, TATpeptide).

Other aspects are described infra.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1 and 2 show Real time PCR results of experiments in which HepG2cells were treated with oligonucleotides designed to target SIRTantisense CV396200. The results show that the levels of the SIRT1 mRNAin HepG2 cells were significantly increased 48 h after treatment withone of the siRNAs designed to sirtas (sirtas_(—)5, P=0.01). In the samesamples the levels of sirtas RNA were significantly decreased aftertreatment with sirtas_(—)5, but unchanged after treatment withsirtas_(—)6 and sirtas_(—)7, which also had no effect on the SIRT1 mRNAlevels (FIG. 2). sirtas_(—)5, sirtas_(—)6 and sirtas_(—)7 correspond toSEQ ID NOs: 47, 48 and 49 respectively.

FIG. 3 shows results for the oligonucleotide walk across the SIRTantisense. Real time PCR results show that the levels of the SIRT1 mRNAin HepG2 cells are significantly increased 48 h after treatment withthree of the antisense oligonucleotides desired to sirtas (CUR-0292,CUR-0307 and CUR-0308). CUR-0292 to CUR-0309 correspond to SEQ ID NOs:24 to 41 respectively.

FIGS. 4 and 5 show results for PS, LNA and 2′O Me Modifiedoligonucleotides in HepG2 (FIG. 4) and Vero76 (FIG. 5) cells. Real timePCR results show that the levels of the SIRT1 mRNA in HepG2 cells aresignificantly increased 48 h after treatment with PS, LNA, 2′O Me and2′O Me mixmer designed antisense oligonucleotides to SIRT1 antisense.Levels of SIRT1 mRNA in Vero cells also increased 48 hours aftertreatment with PS and LNA modified antisense oligonucleotides to SIRT1antisense. Bars denoted as CUR-0245, CUR-0736, CUR 0688, CUR-0740 andCUR-0664 correspond to SEQ ID NOs: 42 to 46 respectively.

FIG. 6 shows PCR results of Monkey Fat Biopsies. Real time PCR resultsshow an increase in SIRT1 mRNA levels in fat biopsies from monkeys dosedwith CUR-963, an oligonucleotide designed to SIRT1 antisense CV396200.1.CUR-963 corresponds to SEQ ID NO: 43.

FIG. 7 shows PCR results of primary monkey liver hepatocytes. Real timePCR results show an increase in SIRT1 mRNA levels after treatment withan oligonucleotide against SIRT1 antisense. Bar denoted as CUR-0245corresponds to SEQ ID NO: 42.

FIG. 8 shows results for oligonucleotides designed to SIRT antisenseCV396200. Real Time PCR results show that levels of SIRT1 mRNA in HepG2cells are significantly increased following treatment with one of theoligonucleotides designed to SIRT1 antisense CV396200. The bars denotedas CUR-1230 to CUR-1233 correspond to SEQ ID NOs: 50 to 53.

FIG. 9 shows results for oligonucleotides designed to SIRT antisenseCV428275. Real Time PCR results show that levels of SIRT1 mRNA in HepG2cells are significantly increased following treatment with two of theoligonucleotides designed to SIRT1 antisense CV428275. The bars denotedas CUR-1302, CUR-1304, CUR-1303 and CUR-1305 correspond to SEQ ID NOs:54 to 57.

FIG. 10 shows Real time PCR results. The results show that a significantincrease in SIRT1 mRNA levels in HepG2 cells 48 hours after treatmentwith one of the oligonucleotides designed to SIRT antisense BE717453.The bars denoted as CUR-1264 to CUR-1266 correspond to SEQ ID NOs: 58 to60 respectively.

FIG. 11 shows Real time PCR results. The results show that show that thelevels of the SIRT1 mRNA in HepG2 cells are significantly increased 48 hafter treatment with three of the oligonucleotides designed to SIRT1antisense AV718812. The bars denoted as CUR-1294, CUR-1297, CUR-1295,CUR-1296 and CUR-1298 correspond to SEQ ID NOs: 61 to 65 respectively.

FIG. 12 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT1 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT1 mRNA are significantly increased at HepG2 cells 48 h aftertreatment with two of the oligos designed to SIRT1 antisense AW169958.Bars denoted as CUR-1381, CUR-1382, CUR-1383 and CUR-1384 correspond tosamples treated with SEQ ID NOS: 66 to 69 respectively.

FIG. 13 is a graph of real time PCR results showing the foldchange+standard deviation, in SIRT1 mRNA after treatment of 3T3 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT1 mRNA are significantly increased in 3T3 cells 48 h aftertreatment with three of the oligonucleotides designed to SIRT1 mouseantisense AK044604. Bars denoted as CUR-0949, CUR-0842, CUR-1098 andCUR-1099 correspond to samples treated with SEQ ID NOS: 76, 70, 80 and81 respectively.

FIG. 14 is a graph of real time PCR results showing the foldchange+standard deviation its SIRT1 mRNA after treatment: of 3T3 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT1 mRNA are significantly increased in 3T3 cells 48 h aftertreatment with five of the oligonucleotides designed to SIRT1 mouseantisense AK044604. Bars denoted as CUR-0948 to CUR-0951, CUR-0846, andCUR-0844 correspond to samples treated with SEQ ID NOS: 75 to 78, 74 and72 respectively.

FIG. 15 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT1 mRNA after treatment of 3T3 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT1 mRNA are significantly increased in HepG2 cells 48 h aftertreatment with two of the oligonucleotides designed to SIRT1 mouseantisense AK044604. Bars denoted as CUR-0842, CUR-0844, and CUR-0845correspond to samples treated with SEQ ID NOS: 70, 72 and 73respectively.

FIG. 16 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT1 mRNA after treatment of 3T3 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT1 mRNA are significantly increased in HepG2 cells 48 h aftertreatment with two of the oligonucleotides designed to SIRT1 mouseantisense AK044604. Bars denoted as CUR-0843 and CUR-0846 correspond tosamples treated with SEQ ID NOS: 71 and 74 respectively.

FIG. 17 is a graph of real time PCR results showing the foldchange+standard deviation in Sirtuin3 mRNA after treatment of HepG2cells with phosphorothioate oligonucleotides introduced usingLipofectamine 2000, as compared to control. RT PCR results show thatsirt3 levels in HepG2 cells are increased 48 hours after treatment withphosphorothioate antisense oligonucleotides designed to sirt3 antisenseHs.683117. Bars denoted as CUR-0551, CUR-1552, CUR-1555, CUR-1556,CUR-1553, CUR-1554, CUR-1545, CUR-1546, CUR-1548, CUR-1549, CUR-1550 andCUR-1547, correspond to samples treated with SEQ ID NOS: 82 to 93respectively.

FIG. 18 is a graph of real time PCR results showing the foldchange+standard deviation in Sirtuin3 mRNA after treatment of HepG2cells with phosphorothioate oligonucleotides introduced usingLipofectamine 2000, as compared to control. RT PCR results show thatsirt3 levels in HepG2 cells are increased 48 hours after treatment withphosphorothioate antisense oligonucleotides designed to sirt3 antisenseBQ024738 and BE164357. Bars denoted as CUR-1869, CUR-1871 and CUR-1873to CUR-1878 correspond to samples treated with SEQ ID NOS: 94, 95, 96and 98, 99, 100, 101 and 102 respectively.

FIG. 19 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT3 mRNA after treatment of Hek293 cellswith phosphorothioate and siRNA oligonucleotides introduced usingLipofectamine 2000, as compared to control. Bars denoted as CUR-1883 andCUR-1884 correspond to samples treated with SEQ ID NOS: 126 and 127respectively.

FIG. 20 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT3 mRNA after treatment of Vero76 cellswith phosphorothioate and siRNA oligonucleotides introduced usingLipofectamine 2000, as compared to control. Bars denoted as CUR-1883CUR-1884 CUR-1873, CUR-1875, CUR-1878 and CUR-1546 correspond to samplestreated with SEQ ID NOS: 126, 127 96, 98, 100, and 92 respectively

FIG. 21 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT4 mRNA after treatment of HUVEC cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1832 and CUR-1835correspond to samples treated with SEQ ID NOS: 105 and 107 respectively.

FIG. 22 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT4 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1833 and CUR-1835correspond to samples treated with SEQ ID NOS: 104 to 107 respectively.

FIG. 23 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT5 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1828, CUR-1829,CUR-1831 and CUR-1830 correspond to samples treated with SEQ ID NOS:108, 109, 111 and 110 respectively.

FIG. 24 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT6 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT6 mRNA in HepG2 cells are significantly increased 48 h aftertreatment with one of the oligos designed to the SIRT6 antisensesequence at accession number NM_(—)133475. Bars denoted as CUR-0873,CUR-0869 to CUR-0871, CUR-0874 and CUR-0872, correspond to samplestreated with SEQ ID NOS: 116, 112, 113, 114, 117 and 115 respectively.

FIG. 25 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT6 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Real time PCR results show that the levelsof SIRT6 mRNA in HepG2 cells are significantly increased 48 h aftertreatment with one of the oligo designed to SIRT6 antisense bf772662.Bars denoted as CUR-0878, CUR-0876, CUR-0877 and CUR-0875, correspond tosamples treated with SEQ ID NOS: 121, 119, 120, and 118 respectively.

FIG. 26 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT6 mRNA after treatment of DBS-FCL-1cells with phosphorothioate oligonucleotides introduced usingLipofectamine 2000, as compared to control. Real time PCR results showthat the levels of SIRT6 mRNA in DBS-FCL-1 cells are significantlyincreased 48 h after treatment with two of the oligos designed to SIRT6antisense bf772662 and one oligo designed to the sequence at accessionnumber NM_133475. Bars denoted as CUR-0876, CUR-0878, CUR-0875 andCUR-0874, correspond to samples treated with SEQ ID NOS: 119, 121, 118and 117 respectively.

FIG. 27 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT7 mRNA after treatment of Vero76 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1824 and CUR-1825correspond to samples treated with SEQ ID NOS: 122 and 123 respectively.

FIG. 28 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT7 mRNA after treatment of SR-N-AS cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1824 and CUR-1825correspond to samples treated with SEQ ID NOS: 124 and 125 respectively.

FIG. 29 is a graph of real time PCR results showing the foldchange+standard deviation in SIRT7 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1824 and CUR-1825correspond to samples treated with SEQ ID NOS: 122 and 123 respectively.

SEQUENCE LISTING DESCRIPTION

SEQ ID NO: 1: Homo sapiens sirtuin (silent mating type informationregulation 2 homolog) 1 (S. cerevisiae) (SIRT1), mRNA (NCBI AccessionNumber: NM_(—)012238.4)

SEQ ID NO: 133: Homo sapiens sirtuin 1 (SIRT1), transcript variant 2,mRNA (NCBI Accession Number: NM_(—)001142498.1)

SEQ ID NO: 2: Mus musoulus sirtuin 1 (silent mating type informationregulation 2, homolog) 1 (S. cerevisiae) (SIRT1) mRNA (NCBI AccessionNumber:NM_(—)001159589)

SEQ ID NO: 3: Homo sapiens sirtuin 2 (SIRT2), transcript variant 1, mRNA(NCBI Accession No.: NM_(—)012237.3).

SEQ ID NO: 134: Homo sapiens sirtuin 2 (SIRT2), transcript variant 2,mRNA (NCBI Accession Number: NM_(—)030593.2)

SEQ ID NO: 135: Homo sapiens sirtuin 2 (SIRT2), transcript variant 3,mRNA (NCBI Accession Number: NM_(—)001193286.1)

SEQ ID NO: 136: Homo sapiens sirtuin 2 (SIRT2), transcript variant 4,non-coding RNA (NCBI Accession Number: NR_(—)134146.1)

SEQ ID NO: 4: Homo sapiens sirtuin (silent mating type informationregulation 2 homolog) 3 (S. cerevisiae) (SIRT3). transcript variant 1,mRNA (NCBI Accession No.: NM_(—)012239.5).

SEQ ID NO: 137: Homo sapiens sirtuin 3 (SIRT3), transcript variant 2,mRNA (NCBI Accession Number: NM_(—)001017524.2)

SEQ ID NO: 5: Homo sapiens sirtuin 4 (SIRT4), mRNA (NCBI Accession No.:NM_(—)012240).

SEQ ID NO: 138: Homo sapiens sirtuin 5 (SIRT5), transcript variant 2,mRNA (NCBI Accession Number: NM_(—)031244.2)

SEQ ID NO: 139: Homo sapiens sirtuin 5 (SIRT5), transcript variant 3,mRNA (NCBI Accession Number: NM_(—)001193267.1)

SEQ ID NO: 6: Homo sapiens sirtuin 5 (SIRT5), transcript variant 1, mRNA(NCBI Accession No.: NM_(—)012241).

SEQ ID NO: 7: Homo sapiens sirtuin 6 (SIRT6), transcript variant 1, mRNA(NCBI Accession No.: NM_(—)016539).

SEQ ID NO: 140: Homo sapiens sirtuin 6 (SIRT6), transcript variant 2,mRNA (NCBI Accession Number: NM_(—)001193285.1)

SEQ ID NO: 8: Homo sapiens sirtuin 7 (SIRT7), mRNA (NCBI Accession No.:NM_(—)016538). Natural Antisense Sequences-SEQ ID NO: 9: Expandednatural antisense sequence (CV396200-expanded); SEQ ID NO: 10: NaturalAntisense sequence (CV428275); SEQ ID NO: 11: Natural Antisense Sequence(BE717453) SEQ ID NO: 12: Natural Antisense Sequence (AV718812); SEQ IDNO: 13: Natural SIRT1 antisense sequence (AW169958): SEQ ID NO: 14:Mouse Natural SIRT1 mouse antisense sequence (AK044604); SEQ ID NO: 15:Natural SIRT3 antisense sequence (Hs.683117); SEQ ID NO: 16: NaturalSIRT3 antisense sequence (DA645474) SEQ ID NO: 17: Natural SIRT3antisense sequence (BQ024738); SEQ ID NO: 18: Natural SIRT3 antisensesequence (BE164357); Natural SIRT3 antisense sequence (RIC8A) SEQ ID NO:141, Natural SIRT3 antisense sequence (PMSD13) SEQ ID NO: 142, NaturalSIRT3 antisense sequence (DA246502) SEQ ID NO: 143, SEQ ID NO: 19:Natural SIRT4 antisense sequence (AA156947); SEQ ID NO: 20: NaturalSIRT5 antisense sequence (Hs.671550); SEQ ID NO: 21: Natural SIRT6antisense sequence (BF772662); SEQ ID NO: 22: Natural SIRT6 antisensesequence (ANKRD24); SEQ ID NO: 23; Natural SIRT7 antisense sequence(Hs.671550) Antisense oligonucleotides-SEQ ID NOs: 24 to 127.* indicatesphosphothioate bond, + indicates LNA and m indicates 2′O Me, r indicatesRNA

SEQ ID NO: 128 to 130-SEQ ID NO: 128 correspond to the exon 4 of theSIRT1 natural antisense CV396200, SEQ ID NO: 129, 130 and 131 correspondto the forward primer sequence, reverse primer sequence and the reportersequence respectively. SEQ ID NO: 132 corresponds to CUR 962, *indicates phosphothioate bond and + indicates LNA.

SEQ ID NO: 144 and 145 correspond to reverse complement of the antisenseoligonucleotide SEQ ID NOS: 126 and 127 respectively.

DETAILED DESCRIPTION

Several aspects of the invention are described below with reference toexample applications for illustration. It should be understood thatnumerous specific details, relationships, and methods are set forth toprovide a full understanding of the invention. One having ordinary skillin the relevant art, however, will readily recognize that the inventioncan be practiced without one or more of the specific details or withother methods. The present invention is not limited by the ordering ofacts or events, as some acts may occur in different orders and/orconcurrently with other acts or events. Furthermore, not all illustratedacts or events are required to implement a methodology in accordancewith the present invention.

All genes, gene names, and gene products disclosed herein are intendedto correspond to homologs from any species for which the compositionsand methods disclosed herein are applicable. Thus, the terms include,but are not limited to genes and gene products from humans and mice. Itis understood that when a gene or gene product from a particular speciesis disclosed, this disclosure is intended to be exemplary only, and isnot to be interpreted as a limitation unless the context in which itappears clearly indicates. Thus, for example, for the genes disclosedherein, which in some embodiments relate to mammalian nucleic acid andamino acid sequences are intended to encompass homologous and/ororthologous genes and gene products from other animals including, butnot limited to other mammals, fish, amphibians, reptiles, and birds. Inembodiments, the genes or nucleic acid sequences are human.

The accession numbers named herein identify publicly available sequencesin the National Institutes of Health database, GenBank (see NucleicAcids Research, 2008 Jan, 36 Database issue: D25-30), unless otherwiseindicated. All sequences referenced by accession number are incorporatedherein by reference.

Definitions

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Furthermore, to the extent that the terms “including”,“includes”, “having”, “has”, “with”, or variants thereof are used ineither the detailed description and/or the claims, such terms areintended to be inclusive in a manner similar to the term “comprising.”

The term “about” or “approximately” means within an acceptable errorrange for the particular value as determined by one of ordinary skill inthe art, which will depend in part on how the value is measured ordetermined, i.e., the limitations of the measurement system. Forexample, “about” can mean within 1 or more than 1 standard deviation,per the practice in the art. Alternatively, “about” can mean a range ofup to 20%, preferably up to 10%, more preferably up to 5%, and morepreferably still up to 1 % of a given value. Alternatively, particularlywith respect to biological systems or processes, the term can meanwithin an order of magnitude, preferably within 5-fold, and morepreferably within 2-fold, of a value. Where particular values aredescribed in the application and claims, unless otherwise slated theterm “about” meaning within an acceptable error range for the particularvalue should be assumed.

As used herein, the term “mRNA” means the presently known mRNAtranscript(s) of a targeted gene, and any further transcripts which maybe elucidated.

By “antisense oligonucleotides” or “antisense compound” is meant an RNAor DNA molecule that binds to another RNA or DNA (target RNA, DNA). Forexample, if it is an RNA oligonucleotide it binds to another RNA targetby means of RNA-RNA interactions and alters the activity of the targetRNA. An antisense oligonucleotide can upregulate or downregulateexpression and/or function of a particular polynucleotide. Thedefinition is meant to include any foreign RNA or DNA molecule which isuseful from a therapeutic, diagnostic, or other viewpoint. Suchmolecules include, for example, antisense RNA or DNA molecules,interference RNA (RNAi), micro RNA, decoy RNA molecules, siRNA,enzymatic RNA, therapeutic editing RNA and agonist and antagonist RNA,antisense oligomeric compounds, antisense oligonucleotides, externalguide sequence (EGS) oligonucleotides, alternate splicers, primers,probes, and other oligomeric compounds that hybridize to at least aportion of the target nucleic acid. As such, these compounds may beintroduced in the form of single-stranded, double-stranded, partiallysingle-stranded, or circular oligomeric compounds.

In the context of this invention, the term “oligonucleotide” refers toan oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleicacid (DNA) or mimetics thereof. The term “oligonucleotide”, alsoincludes linear or circular oligomers of natural and/or modifiedmonomers or linkages, including deoxyribonucleosides, ribonucleosides,substituted and alpha-anomeric forms thereof, peptide nucleic acids(PNA), locked nucleic acids (LNA), phosphorothioate, methylphosphonate,and the like. Oligonucleotides are capable of specifically binding to atarget polynucleotide by way of a regular pattern of monomer-to-monomerinteractions, such as Watson-Crick type of base pairing, Hoögsteen orreverse Hoögsteen types of base pairing, or the like.

The oligonucleotide may be “chimeric”, that is, composed of differentregions. In the context of this invention “chimeric” compounds areoligonucleotides, which contain two or more chemical regions, forexample, DNA region(s), RNA region(s), PNA region(s) etc. Each chemicalregion is made up of at least one monomer unit, i.e., a nucleotide inthe case of an oligonucleotides compound. These oligonucleotidestypically comprise at least one region wherein the oligonucleotide ismodified in order to exhibit one or more desired properties. The desiredproperties of the oligonucleotide include, but are not limited, forexample, to increased resistance to nuclease degradation, increasedcellular uptake, and/or increased binding affinity for the targetnucleic acid. Different regions of the oligonucleotide may thereforehave different properties. The chimeric oligonucleotides of the presentinvention can be formed as mixed structures of two or moreoligonucleotides, modified oligonucleotides, oligonucleosides and/oroligonucleotide analogs as described above.

The oligonucleotide can be composed of regions that can be linked in“register” that is, when the monomers are linked consecutively, as innative DNA, or linked via spacers. The spacers are intended toconstitute a covalent “bridge” between the regions and have in cases alength not exceeding about 100 carbon atoms. The spacers may carrydifferent functionalities, for example, having positive or negativecharge, carry special nucleic acid binding properties (intercalators,groove binders, toxins, fluorophors etc.), being lipophilic, inducingspecial secondary structures like, for example, alanine containingpeptides that induce alpha-helices.

As used herein “Sirtuins (SIRT)s” are inclusive of all family members,mutants, alleles, fragments, species, coding and noncooding sequences,sense and antisense polynucleotide strands, etc.

As used herein, the words Sirtuin 1, SIRT1, sirtuin, silent mating typeinformation regulation 2 homolog 1, hSIR2, hSIRT1, NAD-dependentdeacetylase sirtuin-1, SIR2L1, SIR2-like protein 1, are considered thesame in the literature and are used interchangeably in the presentapplication.

As used herein, the words Sirtuin2, Sirtuin-2, SIRT2, SIR2L and SIR2L2,are considered same in the literature and used interchangeably in thepresent application.

As used herein, the words ‘Sirtuin 3’, Sirtuin3, Sirtuin-3, SIRT3,SIRT-3, hSIRT3, NAD-dependent deacetylase sirtuin-3, mitochondrial,SIR2L3, SIR2-like protein 3 are used interchangeably in the presentapplication.

As used herein, the words Sirtuin4, SIRT4, MGC130046, MGC130047,MGC57437, NAD-dependent ADP-ribosyltransferase sirtuin-4, SIR2L4,SIR2-like protein 4, are considered same in the literature and usedinterchangeably in the present application.

As used herein, the words Sirtuin 5, SIRT5, FLJ36950, NAD-dependentdeacetylase sirtuin-5, SIR2L5, SIR2-like protein 5, are considered samein the literature and used interchangeably in the present application.

As used herein, the words ‘Sirtuin 6’, Sirtuin6, Sirtuin-6, SIRT6,SIRT-6, NAD-dependent deacetylase sirtuin-6, SIR2L6, SIR2-like protein 6are considered the same in the literature and are used interchangeablyin the present application.

As used herein, the words Sirtuin 7, SIRT7, MGC126840, MGC126842,NAD-dependent deacetylase sirtuin-7, SIR2L7, SIR2-like protein 7, areconsidered same in the literature and used interchangeably in thepresent application.

As used herein, the term “oligonucleotide specific for” or“oligonucleotide which targets” refers to an oligonucleotide having asequence (i) capable of forming a stable complex with a portion of thetargeted gene, or (ii) capable of forming a stable duplex with a portionof a mRNA transcript of the targeted gene. Stability of the complexesand duplexes can be determined by theoretical calculations and/or invitro assays. Exemplary assays for determining stability ofhybridization complexes and duplexes are described in the Examplesbelow.

As used herein, the term “target nucleic acid” encompasses DNA, RNA(comprising premRNA and mRNA) transcribed from such DNA, and also cDNAderived from such RNA, coding, noncoding sequences, sense or antisensepolynucleotides. The specific hybridization of an oligomeric compoundwith its target nucleic acid interferes with the normal function of thenucleic acid. This modulation of function of a target nucleic acid bycompounds, which specifically hybridize to it, is generally referred toas “antisense”. The functions of DNA to be interfered include, forexample, replication and transcription. The functions of RNA to beinterfered, include all vital functions such as, for example,translocation of the RNA to the site of protein translation, translationof protein from the RNA, splicing of the RNA to yield one or more mRNAspecies, and catalytic activity which may be engaged in or facilitatedby the RNA. The overall effect of such interference with target nucleicacid function is modulation of the expression of an encoded product oroligonucleotides.

RNA interference “RNAi” is mediated by double stranded RNA (dsRNA)molecules that have sequence-specific homology to their “target” nucleicacid sequences. In certain embodiments of the present invention, themediators are 5-25 nucleotide “small interfering” RNA duplexes (siRNAs).The siRNAs are derived from the processing of dsRNA by an RNase enzymeknown as Dicer. siRNA duplex products are recruited into a multi-proteinsiRNA complex termed RISC (RNA Induced Silencing Complex). Withoutwishing to be bound by any particular theory, a RISC is then believed tobe guided to a target nucleic acid (suitably mRNA), where the siRNAduplex interacts in a sequence-specific way to mediate cleavage in acatalytic fashion. Small interfering RNAs that can be used in accordancewith the present invention cast be synthesized and used according toprocedures that are well known in the art and that will be familiar tothe ordinarily skilled artisan. Small interfering RNAs for use in themethods of the present invention suitably comprise between about 1 toabout 50 nucleotides (nt). In examples of non limiting embodiments,siRNAs can comprise about 5 to about 40 nt, about 5 to about 30 nt,about 10 to about 30 nt, about 15 to about 25 nt, or about 20-25nucleotides.

Selection of appropriate oligonucleotides is facilitated by usingcomputer programs that automatically align nucleic acid sequences andindicate regions of identity or homology. Such programs are used tocompare nucleic acid sequences obtained, for example, by searchingdatabases such as GenBank or by sequencing PCR products. Comparison ofnucleic acid sequences from a range of species allows the selection ofnucleic acid sequences that display an appropriate degree of identitybetween species. In the case of genes that have not been sequenced.Southern blots are performed to allow a determination of the degree ofidentity between genes in target species and other species. Byperforming Southern blots at varying degrees of stringency, as is wellknown in the art, it is possible to obtain an approximate measure ofidentity. These procedures allow the selection of oligonucleotides thatexhibit a high degree of complementarity to target nucleic acidsequences in a subject to be controlled and a lower degree ofcomplementarity to corresponding nucleic acid sequences in otherspecies. One skilled in the art will realize that there is considerablelatitude in selecting appropriate regions of genes for use in thepresent invention.

By “enzymatic RNA” meant an RNA molecule with enzymatic activity.Enzymatic nucleic acids (ribozymes) act by first binding to a targetRNA. Such binding occurs through the target binding portion of anenzymatic nucleic acid which is held in close proximity to an enzymaticportion of the molecule that acts to cleave the target RNA. Thus, theenzymatic nucleic acid first recognizes and then binds a target RNAthrough base pairing, and once bound to the correct site, actsenzymatically to cut the target RNA.

By “decoy RNA” is meant an RNA molecule that mimics the natural bindingdomain for a ligand. The decoy RNA therefore competes with naturalbinding target for the binding of a specific ligand. For example, it hasbeen shown that over-expression of HIV trans-activation response (TAR)RNA can act as a “decoy” and efficiently binds HIV tat protein, therebypreventing it from binding to TAR sequences encoded in the HIV RNA. Thisis meant to be a specific example. Those in the art will recognize thatthis is but one example, and other embodiments can be readily generatedusing techniques generally known in the art.

As used herein, the term “monomers” typically indicates monomers linkedby phosphodiester bonds or analogs thereof to form oligonucleotidesranging in size from a few monomeric units, e.g., from about 3-4, toabout several hundreds of monomeric units. Analogs of phosphodiesterlinkages include: phosphorothioate, phosphorodithioate,methylphosphomates, phosphoroselenoate, phosphoramidate, and the like,as more fully described below.

The term “nucleotide” covers naturally incurring nucleotides as well asnon-naturally occurring nucleotides. It should be clear to the personskilled in the art that various nucleotides which previously have beenconsidered “non-naturally occurring” have subsequently been found innature. Thus, “nucleotides” includes not only the known purine andpyrimidine heterocycles-containing molecules, but also heterocyclicanalogues and tautomers thereof. Illustrative examples of other types ofnucleotides are molecules containing adenine, guanine, thymine,cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo-N6-methyladenine, 7-deazaxanthine, 7-deazaguanine, N4,N4-ethanocytosin,N6,N6-ethano-2,6-diaminopurine, 5-methylcytosine, 5-(C3-C6)-alkynylcytosine, 5-flourouracil, 5-bromouracil, pseudoisocytosine,2-hydroxy-5-methyl-4-triazolopyridin, isocytosine, isoguanin, inosineand the “non-naturally occurring” nucleotides described in U.S. Pat. No.5,432,272. The term “nucleotide” is intended to cover every and all ofthese examples as well as analogues and tautomers thereof. Especiallyinteresting nucleotides are those containing adenine, guanine, thymine,cytosine, and uracil, which are considered as the naturally occurringnucleotides in relation to therapeutic and diagnostic application inhumans. Nucleotides include the natural 2′-deoxy and 2′-hydroxyl sugars,e.g., as described in Kornberg and Baker, DNA Replication, 2nd Ed.(Freeman, San Francisco, 1992) as well as their analogs.

“Analogs” in reference to nucleotides includes synthetic nucleotideshaving modified base moieties and/or modified sugar moieties. Suchanalogs include synthetic nucleotides designed to enhance bindingproperties, e.g., duplex or triplex stability, specificity, or the like.

As used herein, “hybridization” means the pairing of substantiallycomplementary strands of oligomeric compounds. One mechanism of pairinginvolves hydrogen bonding, which may be Watson-Crick, Hoögsteen orreversed Hoögsteen hydrogen bonding, between complementary nucleoside ornucleotide bases (nucleotides) of the strands of oligomeric compounds.For example, adenine and thymine are complementary nucleotides whichpair through the formation of hydrogen bonds. Hybridization can occurunder varying circumstances.

An antisense compound is “specifically hybridizable” when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a modulation of function and/oractivity, and there is a sufficient degree of complementarity to avoidnon-specific binding of the antisense compound to non-target nucleicacid sequences under conditions in which specific binding is desired,i.e., under physiological conditions in the case of in vivo assays ortherapeutic treatment, and under conditions in which assays areperformed in the case of in vitro assays.

As used herein, the phrase “stringent hybridization conditions” or“stringent conditions” refers to conditions under which a compound ofthe invention will hybridize to its target sequence, but to a minimalnumber of other sequences. Stringent conditions are sequence-dependentand will be different in different circumstances and in the context ofthis invention, “stringent conditions” under which oligomeric compoundshybridize to a target sequence are determined by the nature andcomposition of the oligomeric compounds and the assays in which they arebeing investigated. In general, stringent hybridization conditionscomprise low concentrations (<0.15 M) of salts with inorganic cationssuch as Na++ or K++ (i.e., low ionic strength), temperature higher than20° C.-25° C. below the Tm of the oligomeric compound:target sequencecomplex, and the presence of denaturants such as formamide,dimethylformamide, dimethyl sulfoxide, or the detergent sodium dodecylsulfate (SDS). For example, the hybridization rate decreases 1.1% foreach 1% formamide. An example of a high stringency hybridizationcondition is 0.1× sodium chloride-sodium citrate buffer (SSC)/0.1% (w/v)SDS at 60° C. for 30 minutes.

“Complementary,” as used herein, refers to the capacity for precisepairing between two nucleotides on one or two oligomeric strands. Forexample, if a nucleobase at a certain position of an antisense compoundis capable of hydrogen bonding with a nucleobase at a certain positionof a target nucleic acid, said target nucleic acid being a DNA, RNA, oroligonucleotide molecule, then the position of hydrogen bonding betweenthe oligonucleotide and the target nucleic acid is considered to be acomplementary position. The oligomeric compound and the further DNA,RNA, or oligonucleotide molecule are complementary to each other when asufficient number of complementary positions in each molecule areoccupied by nucleotides which can hydrogen bond with each other. Thus,“specifically hybridizable” and “complementary” are terms which are usedto indicate a sufficient degree of precise pairing or complementarityover a sufficient number of nucleotides such that stable and specificbinding occurs between the oligomeric compound and a target nucleicacid.

It is understood in the art that the sequence of an oligomeric compoundneed not be 100% complementary to that of its target nucleic acid to bespecifically hybridizable. Moreover, an oligonucleotide may hybridizeover one or more segments such that intervening or adjacent segments arenot involved in the hybridization event (e.g., a loop structure,mismatch or hairpin structure). The oligomeric compounds of the presentinvention comprise at least about 70%, or at least about 75%, or atleast about 80%, or at least about 85%, or at least about 90%, or atleast about 95%, or at least about 99% sequence complementarity to atarget region within the target nucleic acid sequence to which they aretargeted. For example, an antisense compound in which 18 of 20nucleotides of the antisense compound tire complementary to a targetregion, and would therefore specifically hybridize, would represent 90percent complementarity. In this example, the remaining noncomplementarynucleotides may be clustered or interspersed with complementarynucleotides and need not be contiguous to each other or to complementarynucleotides. As such, an antisense compound which is 18 nucleotides inlength having 4 (four) noncomplementary nucleotides which are flanked bytwo regions of complete complementarity with the target nucleic acidwould have 77.8% overall complementarity with the target nucleic acidand would thus fall within the scope of the present invention. Percentcomplementarity of an antisense compound with a region of a targetnucleic acid can be determined routinely using BLAST programs (basiclocal alignment search tools) and PowerBLAST programs known in the art.Percent homology, sequence identity or complemenlarity, can bedetermined by, for example, the Gap program.

As used herein, the term “Thermal Melting Point (Tm)” refers to thetemperature, under defined ionic strength, pH, and nucleic acidconcentration, at which 50% of the oligonucleotides complementary to thetarget sequence hybridize to the target sequence at equilibrium.Typically, stringent conditions will be those in which the saltconcentration is at least about 0.01 to 1.0 M Na ion concentration (orother salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C. for short oligonucleotides (e.g., 10 to 50 nucleotide). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide.

As used herein, “modulation” means either an increase (stimulation) or adecrease (inhibition) in the expression of a gene.

The term “variant,” when used in the context of a polynucleotidesequence, may encompass a polynucleotide sequence related to a wild typegene. This definition may also include, for example, “allelic,”“splice,” “species,” or “polymorphic” variants. A splice variant mayhave significant identity to a reference molecule, but will generallyhave a greater or lesser number of polynucleotides due to alternatesplicing of exons during mRNA processing. The corresponding polypeptidemay possess additional functional domains or an absence of domains.Species variants are polynucleotide sequences that vary from one speciesto another. Of particular utility in the invention are variants of wildtype gene products. Variants may result from at least one mutation inthe nucleic acid sequence and may result in altered mRNAs or inpolypeptides whose structure or function may or may not be altered. Anygiven natural or recombinant gene may have none, one, or many allelicforms. Common mutational changes that give rise to variants aregenerally ascribed to natural deletions, additions, or substitutions ofnucleotides. Each of these types of changes may occur alone, or incombination with the others, one or more times in a given sequence.

The resulting polypeptides generally will have significant amino acididentity relative to each other. A polymorphic variant is a variation inthe polynucleotide sequence of a particular gene between individuals ofa given species. Polymorphic variants also may encompass “singlenucleotide polymorphisms” (SNPs,) or single base mutations in which thepolynucleotide sequence varies by one base. The presence of SNPs may beindicative of, for example, a certain population with a propensity for adisease state, that is susceptibility versus resistance.

Derivative polynucleotides include nucleic acids subjected to chemicalmodification, for example, replacement of hydrogen by an alkyl, acyl, oramino group. Derivatives, e.g. derivative oligonucleotides, may comprisenon-naturally-occurring portions, such as altered sugar moieties orinter-sugar linkages. Exemplary among these are phosphorothioate andother sulfur containing species which are known in the art. Derivativenucleic acids may also contain labels, including radionucleotides,enzymes, fluorescent agents, chemiluminescent agents, chromogenicagents, substrates, cofactors, inhibitors, magnetic particles, and thelike.

A “derivative” polypeptide or peptide is one that is modified, forexample, by glycosylation, pegylation, phosphorylation, sulfation,reduction/alkylation, acylation, chemical coupling, or mild formalintreatment. A derivative may also be modified to contain a detectablelabel, either directly or indirectly, including, but not limited to, aradioisotope, fluorescent, and enzyme label.

As used herein, the term “animal” or “patient” is meant to include, forexample, humans, sheep, elks, deer, mule deer, minks, mammals, monkeys,horses, cattle, pigs, goats, dogs, cats, rats, mice, birds, chicken,reptiles, fish, insects and arachnids.

“Mammal” covers warm blooded mammals that are typically under medicalcare (e.g., humans and domesticated animals). Examples include feline,canine, equine, bovine, and human, as well as just human.

“Treating” or “treatment” covers the treatment of a disease-state in amammal, and includes: (a) preventing the disease-state from occurring ina mammal, in particular, when such mammal is predisposed to thedisease-state but has not yet been diagnosed as having it; (b)inhibiting the disease-state, e.g., arresting it development; and/or (c)relieving the disease-state, e.g., causing regression of the diseasestate until a desired endpoint is reached. Treating also includes theamelioration of a symptom of a disease (e.g., lessen the pain ordiscomfort), wherein such amelioration may or may not be directlyaffecting the disease (e.g., cause, transmission, expression, etc).

As used herein, “cancer” refers to all types of cancer or neoplasm ormalignant tumors found in mammals, including, but not limited to:leukemias, lymphomas, melanomas, carcinomas and sarcomas. The cancermanifests itself as a “tumor” or tissue comprising malignant cells ofthe cancer. Examples of tumors include sarcomas and carcinomas such as,but not limited to: fibrosarcoma, myxosarcoma, liposarcoma,chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma,synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma,rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer,ovarian cancer, prostate cancer, squamous cell carcinoma, basal cellcarcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous glandcarcinoma, papillary carcinoma, papillary adenocarcinomas,cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renalcell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma,seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testiculartumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma,epithelial carcinoma, glioma, astrocytoma, medulloblastoma,craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acousticneuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, andretinoblastoma. Additional cancers which can be treated by the disclosedcomposition according to the invention include but not limited to, forexample. Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma,neuroblastoma, breast cancer, ovarian cancer, lung cancer,rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia,small-cell lung tumors, primary brain tumors, stomach cancer, coloncancer, malignant pancreatic insulanoma, malignant carcinoid, urinarybladder cancer, premalignant skin lesions, testicular cancer, lymphomas,thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tractcancer, malignant hypercalcemia, cervical cancer, endometrial cancer,adrenal cortical cancer, and prostate cancer.

“Neurological disease or disorder” refers to any disease or disorder ofthe nervous system and/or visual system, “Neurological disease ordisorder” include disease or disorders that involve the central nervoussystem (brain, brainstem and cerebellum), the peripheral nervous system(including cranial nerves), and the autonomic nervous system (parts ofwhich are located in both central and peripheral nervous system).Examples of neurological disorders include but are not limited to,headache, stupor and coma, dementia, seizure, sleep disorders, trauma,infections, neoplasms, neuroopthalmology, movement disorders,demyelinatiag diseases, spinal cord disorders, and disorders ofperipheral nerves, muscle and neuromuscular junctions. Addiction andmental illness, include, but are not limited to, bipolar disorder andschizophrenia, are also included in the definition of neurologicaldisorder. The following is a list of several neurological disorders,symptoms, signs and syndromes that can be treated using compositions andmethods according to the present invention: acquired epileptiformaphasia; acute disseminated encephalomyelitis; adrenoleukodystrophy;age-related macular degeneration; agenesis of the corpus callosum;agnosia; Aicardi syndrome; Alexander disease; Alpers' disease;alternating hemiplegia; Vascular dementia; amyotrophic lateralsclerosis; anencephaly; Angelman syndrome; angiomatosis; anoxia;aphasia; apraxia; arachnoid cysts; arachnoiditis; Anronl-Chiarimalformation; arteriovenous malformation; Asperger syndrome; ataxiatelegiectasia; attention deficit hyperactivity disorder; autism;autonomic dysfunction; back pain; Batten disease; Behcet's disease;Bell's palsy; benign essential blepharospasm; benign focal; amyotrophy;benign intracranial hypertension; Binswanger's disease; blepharospasm;Bloch Sulzberger syndrome; brachial plexus injury; brain abscess; braininjury; brain tumors (including glioblastoma multiforme); spinal tumor;Brown-Sequard syndrome; Canavan disease; carpal tunnel syndrome;causalgia; central pain syndrome; central pontine myelinolysis; cephalicdisorder; cerebral aneurysm; cerebral arteriosclerosis; cerebralatrophy; cerebral gigantism; cerebral palsy; Charcot-Marie-Toot disease;chemotherapy-induced neuropathy and neuropathic pain; Chiarimalformation; chorea; chronic inflammatory demyelinating polyneuropathy;chronic pain; chronic regional pain syndrome; Coffin Lowry syndrome;coma, including persistent vegetative state; congenital facial diplegia;corticobasal degeneration; cranial arteritis; craniosynostosis;Creutzfeldt-Jakob disease; cumulative trauma disorders; Cushing'ssyndrome; cytomegalic inclusion body disease; cytomegalovirus infection;dancing eyes-dancing feet syndrome; Dandy Walker syndrome; Dawsondisease; De Morsier's syndrome; Dejerine-Klumke palsy; dementia;dermatomyositis; diabetic neuropathy; diffuse sclerosis; dysautonomia;dysgraphia; dyslexia; dystonias; early infantile epilepticencephalopathy; empty sella syndrome; encephalitis; encephaloceles;encephalotrigeminal angiomatosis; epilepsy; Erb's palsy; essentialtremor; Fabry's disease; Fahr's syndrome; fainting; familial spasticparalysis; febrile seizures; fisher syndrome; Friedreich's ataxia;fronto-temporal dementia and other “tauopathies”; Gaucher's disease;Gerstmann's syndrome; giant cell arteritis; giant cell inclusiondisease; globoid cell leukodystrophy; Guillain-Barre syndrome;HTLV-1-associated myelopathy; Hallervorden-Spate disease; head injury;headache; hemifacial spasm; hereditary spastic paraplegia; heredopathiaatactic a polyneoritiformis; herpes zoster oticus; herpes zoster;Hirayama syndrome; HIV associated dementia and neuropathy (alsoneurological manifestations of AIDS); holoprosencephaly; Huntington'sdisease and other polyglutamine repeat diseases; hydranencephaly;hydrocephalus; hypercortisolism; hypoxia; immune-mediatedencephalomyelitis; inclusion body myositis; incontinentia pigment;infantile phytanic acid storage disease; infantile refsum disease;infantile spasms; inflammatory myopathy; intracranial cyst; intracranialhypertension; Joubert syndrome; Keams-Sayre syndrome; Kennedy diseaseKinsbourne syndrome; Klippel Feil syndrome; Krabbe disease;Kugelberg-Welander disease; kuru; Lafora disease; Lambert-Eatonmyasthenic syndrome; Landau-Kleffner syndrome; lateral medullary(Wallenberg) syndrome; learning disabilities; Leigh's disease;Lennox-Gustaut syndrome; Lesch-Nyhan syndrome; leukodystrophy; Lewy bodydementia; Lissencephaly; locked-in syndrome; Lou Gehrig's disease (i.e.,motor neuron disease or amyotrophic lateral sclerosis); lumbar discdisease; Lyme disease-neurological sequelae; Machado-Joseph disease;macrencephaly; megalencephaly; Melkersson-Rosenthal syndrome; Menieresdisease; meningitis; Menkes disease; metachromatic leukodystrophy;microcephaly; migraine; Miller Fisher syndrome; mini-strokes;mitochondrial myopathies; Mobius syndrome; monomelic amyotrophy; motorneuron disease; Moyamoya disease; mucopolysaccharidoses; milti-infarctdementia; multifocal motor neuropathy; multiple sclerosis and otherdemyelinating disorders; multiple system atrophy with posturalhypotension; p muscular dystrophy; myasthenia gravis; myelinoclasticdiffuse sclerosis; myoclonic encephalopathy of infants; myoclonus;myopathy; myotonia congenital; narcolepsy; neurofibromatosis;neuroleptic malignant syndrome; neurological manifestations of AIDS;neurological sequelae of lupus; neuromyotonia; neuronal ceroidlipofuscinosis; neuronal migration disorders; Niemann-Pick disease;O'Sullivan-McLeod syndrome; occipital neuralgia; occult spinaldysraphism sequence; Ohtahara syndrome; olivopontocerebellar atrophy;opsoclonus myoclonus; optic neuritis; orthostatic hypotension; overusesyndrome; paresthesia; Neurodegenerative disease or disorder(Parkinson's disease, Huntington's disease, Alzheimer's disease,amyotrophic lateral sclerosis (ALS), dementia, multiple sclerosis andother diseases and disorders associated with neuronal cell death);paramyotonia congenital; paraneoplastic diseases; paroxysmal attacks;Parry Romberg syndrome; Pelizaeus-Merzbacher disease; periodicparalyses; peripheral neuropathy; painful neuropathy and neuropathicpain; persistent vegetative state; pervasive developmental disorders;photic sneeze reflex; phytanic acid storage disease; Pick's disease;pinched nerve; pituitary tumors; polymyositis; porencephaly; post-poliosyndrome; posterpetic neuralgia; postinfectious encephalomyelitis;postural hypotension; Prader-Willi syndrome; primary lateral sclerosis;prion diseases; progressive hemifacial atrophy; progressivemultifocallcukoencephalopathy; progressive sclerosing poliodystrophy;progressive supranuclear palsy; pseudotumor cerebri; Ramsay-Huntsyndrome (types I and II); Rasmussen's encephalitis; reflex sympatheticdystrophy syndrome; Refsum disease; repetitive motion disorders;repetitive stress injuries; restless legs syndrome;retrovirus-associated myelopathy; Rett syndrome; Reye's syndrome; SaintVitus dance; Sandhoff disease; Schilder's disease; schizencephaly;septo-optic dysplasia; shaken baby syndrome; shingles; Shy-Dragersyndrome; Sjogren's syndrome; sleep apnea; Soto's syndrome; spasticity;spina bifida; spinal cord injury; spinal cord tumors; spinal muscularatrophy; Stiff-Person syndrome; stroke; Sturge-Weber syndrome; subacutesclerosing panencephalitis; subcortical arteriosclerotic,encephalopathy; Sydenham chorea; syncope; syringomyelia; tardivedyskinesia; Tay-Sachs disease; temporal arteritis; tethered spinal cordsyndrome; Thomsen disease; thoracic outlet syndrome; Tic Douloureux;Todd's paralysis; Tourette syndrome; transient ischemic attack;transmissible spongiform encephalopathies; transverse myelitis;traumatic brain injury; tremor; trigeminal neuralgia; tropical spasticparaparesis; tuberous sclerosis; vascular dementia (multi-infarctdementia); vasculitis including temporal arteritis; Von Hippel-Lindaudisease; Wallenberg's syndrome; Werdnig-Hoffman disease; West syndrome;whiplash; Williams syndrome; Wildon's disease; and Zellweger syndrome.

“Metabolic disease” refers to a wide range of diseases and disorders ofthe endocrine system including, for example, insulin resistance,diabetes, obesity, impaired glucose tolerance, high blood cholesterol,hyperglycemia, dyslipidemia and hyperlipidemia.

An “Inflammation” refers to systemic inflammatory conditions andconditions associated locally with migration and attraction ofmonocytes, leukocytes and/or neutrophils. Examples of inflammationinclude, but are not limited to, Inflammation resulting from infectionwith pathogenic organisms (including grant-positive bacteria,gram-negative bacteria, viruses, fungi, and parasites such as protozoaand helminths), transplant rejection (including rejection of solidorgans such as kidney, liver, heart, lung or cornea, as well asrejection of bone marrow transplants including graft-versus-host disease(GVHD)), or from localized chronic or acute autoimmune or allergicreactions. Autoimmune diseases include acute glomerulonephritis;rheumatoid or reactive arthritis; chronic glomerulonephritis;inflammatory bowel diseases such as Crohn's disease, ulcerative colitisand necrotizing enterocolitis; granulocyte transfusion associatedsyndromes; inflammatory dermatoses such as contact dermatitis, atopicdermatitis, psoriasis; systemic lupus erythematosus (SLE), autoimmunethyroiditis, multiple sclerosis, and some forms of diabetes, or anyother autoimmune state where attack by the subject's own immune systemresults in pathologic tissue destruction. Allergic reactions includeallergic asthma, chronic bronchitis, acute and delayed hypersensitivity.Systemic inflammatory disease states include inflammation associatedwith trauma, burns, reperfusion following ischemic events (e.g.thrombotic events in heart, brain, intestines or peripheral vasculature,including myocardial infarction and stroke), sepsis, ARDS or multipleorgan dysfunction syndrome. Inflammatory cell recruitment also occurs inaterosclerotic plaques. Inflammation includes, but is not limited to,Non-Hodgkin's lymphoma, Wegener's granulomatosis, Hashimoto'sthyroiditis, hepatocellular carcinoma, thymus atrophy, chronicpancreatitis, rheumatoid arthritis, reactive lymphoid hyperplasia,osteoarthritis, ulcerative colitis, papillary carcinoma, Crohn'sdisease, ulcerative colitis, acute cholecystitis, chronic cholecystitis,cirrhosis, chronic sialadenitis, peritonitis, acute pancreatitis,chronic pancreatitis, chronic Gastritis, adenomyosis, endometriosis,acute cervicitis, chronic cervicitis, lymphoid hyperplasia, multiplesclerosis, hypertrophy secondary to idiopathic thrombocytopenic purpura,primary IgA nephropathy, systemic lupus erythematosus, psoriasis,pulmonary emphysema, chronic pyelonephritis, and chronic cystitis.

A ‘cardiovascular disease or disorder’ includes those disorders that caneither cause ischemia or are caused by reperfusion of the heart.Examples include, but are not limited to, atherosclerosis, coronaryartery disease, granulomatous myocarditis, chronic myocarditis(non-granulomatous), primary hypertrophic cardiomyopathy, peripheralartery disease (PAD), stroke, angina pectoris, myocardial infarction,cardiovascular tissue damage caused by cardiac arrest, cardiovasculartissue damage caused by cardiac bypass, cardiogenic shock, and relatedconditions that would be known by those of ordinary skill in the art orwhich involve dysfunction of or tissue damage to the heart orvasculature, especially, but not limited to, tissue damage related toSirtuin3 activation. CVS diseases include, but are not limited to,atherosclerosis, granulomatous myocarditis, myocardial infarction,myocardial fibrosis secondary to valvular heart disease, myocardialfibrosis without infarction, primary hypertrophic cardiomyopathy, andchronic myocarditis (non-granulomatous).

Polynucleotide and Oligonucleotide Compositions and Molecules Targets

In one embodiment, the targets comprise nucleic acid sequences of aSirtuin (SIRT), including without limitation sense and/or antisensenoncoding and/or coding sequences associated with a Sirtuin (SIRT).

In one embodiment, the targets comprise nucleic acid sequences of SIRT1,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT1gene.

In one embodiment, the targets comprise nucleic acid sequences of SIRT2,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT2 gene.

In one embodiment, she targets comprise nucleic acid sequences of SIRT3,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT3 gene.

In one embodiment, the targets comprise nucleic acid sequences of SIRT4,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT4 gene.

In one embodiment, the targets comprise nucleic acid sequences of SIRT5,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT5 gene.

In one embodiment, the targets comprise nucleic acid sequences of SIRT6,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT6 gene.

In one embodiment, the targets comprise nucleic acid sequences of SIRT7,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SIRT7 gene.

“SIRT1 protein” refers to a member of the sir2 family of sirtuindeacetylases. In one embodiment, a SIRT1 protein includes yeast Sir2(GenBank Accession No. P53685), C. elegans Sir-2,1 (GenBank AccessionNo. NP.sub.-501912), human SIRT1. (GenBank Accession No. NM.sub.-012238and NP,snb.-036370 (or AF083106))

SIRT1 “Sirtuins” are proteins that include a SIR2 domain, a domaindefined as amino acids sequences that are scored as hits in the Plantfamily “SIR2”-PF02146 (attached to the Appendix). This family isreferenced in the INTERPRO database as INTERPRO description (entryIPR003000). To identify the presence of a “SIR2” domain in a proteinsequence, and make the determination that a polypeptide or protein ofinterest has a particular profile, the amino acid sequence of theprotein can be searched against the Pfam database of HMMs (e.g., thePfam database, release 9) using the default parameters(http://www.sanger.ac.uk/Software/Pfam/HMM_search). The SIR2 domain isindexed in Pfam as PF02146 and in INTERPRO as INTERPRO description(entry IPR003000). A description of the Pfam database can be found in“The Pfam Protein Families Database” Bateman A et al. (2002) NucleicAcids Research 30(1):276-280 and Sonhammer et al. (1997) Proteins28(3):405-420 and a detailed description of HMMs can be found, forexample, in Gribskov et al. (1990) Meth. Enzymol. 183:146-159; Gribskovet al. (1987) Proc. Natl. Acad. Sci. USA 84:4355-4358; Krogh et al.(1994) J. Mol. Biol. 235:1501-1531; and Stultz et al. (1993) ProteinSci. 2:305-314.

Among the mitochondrial sirtuins, SIRT3 possesses the most robustdeacetylase activity. Indeed, significantly higher levels ofmitochondrial protein acetylation were detected in the livers ofSIRT3-null mice, compared to those of SIRT4 or SIRT5 knockout animals.However, little is known about the physiological role of SIRT3 despitethe fact that a number of SIRT3 substrates and co-precipitating proteinshave been identified: acetyl-CoA synthetase 2, Ku70, FOXO3a, subunit 9of mitochondrial Complex I (NDUFA9), glutamate dehydrogenase andisocitrate dehydrogenase 2.

SIRT3 is a major mitochondrial deacetylase. Mitochondrial proteins showhyperacetylation in SIRT3 knockout mice, but not in SIRT4 or SIRT5knockout mice. Acetyl-CoA synthetase 2 (AceCS2), a mitochondrial enzymethat converts acetate into acetyl-CoA, was the first mitochondrialsubstrate of SIRT3 identified. Deacetylation of AccCS2 at lysine 642 bySIRT3 activates acetyl-CoA synthetase activity, providing increasedacetyl-CoA to feed into the tricarboxylic acid cycle. Glutamatedehydrogenase (GDH), another mitochondrial protein involved in energyproduction, is deacetylated by SIRT3. GDH can also be ADP-ribosylated bySIRT4 in turn to decrease its enzyme activity. This indicates that SIRT3could play an important role in cell metabolism. SIRT3 has also beenshown to be involved in selective apoptosis pathways and cell growthcontrol SIRT3 and SIRT4, but not SIRT5, have been implicated in the NAD+salvage pathway that regulates the NAD+ level relating to cell survival.In addition, variability in the hSIRT3 gene has been linked to humanlongevity.

The Silent Information Regulator-2 gene (Sir2) encodes an NAD-dependenthistone deacetylase that links regulation of chromatin, genomicstability, and life span in S. cerevisae. By promoting chromatinsilencing, Sir2 inhibits transcription at several genetic loci andrepresses recombination at ribosomal DNA (rDNA) repeats. Yeast withmutations in Sir2 have increased genomic instability in the context ofrDNA recombination, which in turn shortens replicative life span—amarker of reproductive aging in this organism. Conversely, extracopiesof Sir2 that suppress rDNA recombination increase replicative life span.These effects of Sir2 suggest paradigms in which genes that promotegenome stabilization through chromatin modulation may be importantcontributors to regulation organismal life span, aging, and age-relatedpathology.

Consistent with a conserved role for Sir2 factors in life spanregulation, increased activity of Sir2 proteins in the multicellularorganisms C. elegans and D. melanogaster also increases life span.However, these Sir2 factors may operate through mechanisms that areindependent of genome stabilization, and their physiologic molecularsubstrates are still unclear. In mammals, there are seven Sir2 familymembers, SIRT1-SIRT7. The SIRTs have been of great interest as candidateregulate of mammalian life span and aging-related processes. In thiscontext, several mammalian SIRTs have functions that impact onaging-associated molecular pathways and disease. However, initialstudies of mammalian SIRTs linked these enzymes to biochemical targetsand cellular functions that are distinct from those of S. cerevisiaeSir2.

Sirtuins are homologues of the yeast transcriptional repressor Sir2p andare conserved from bacteria to humans. Human SIRT4 is localized to themitochondria. SIRT4 is a matrix protein and becomes cleaved at aminoacid 28 after import into mitochondria. Mass spectrometry analysis ofproteins that coimmunoprecipitate with SIRT4 identified insulindegrading enzyme and the ADP/ATP carrier proteins, ANT2 and ANT3. SIRT4exhibits no histone deacetylase activity but functions as an efficientADP-ribosyltransferase on histones and bovine serum albumin. SIRT4 isexpressed in islets of Langerhans and colocalizes withinsulin-expressing β cells. Depletion of SIRT4 from insulin-producingINS-1E cells results in increased insulin secretion in response toglucose.

Sirtuin (silent mating type information regulation 2 homology) 5 (S.cerevisae), also known as SIRT5 is a protein which in humans in encodedby the SIRT5 gene and in other species by the Sirt5 gene. This geneencodes a member of the sirtuin family of proteins, homologs to theyeast Sir2 protein. Members of the sirtuin family are characterized by asirtuin core domain and grouped into four classes. The functions ofhuman sirtuins have not yet been determined; however, yeast sirtuinproteins are known to regulate epigenetic gene silencing and suppressrecombination of rDNA. Studies suggest that the human sirtuins mayfunction as intracellular regulatory proteins withmono-ADP-ribosyltransferase activity. The protein encoded by this geneis included in class III of the sirtuin family. Alternative splicing ofthis gene results in two transcript variants.

The generation of mice deficient for the mammalian SIRT6 gene revealed apotential role for SIRT6 in linking regulation of life span, chromatin,and genomic stability. In this context, SIRT6 deficiency in mice leadsto dramatically shortened life span and acute degenerative phenotypesthat overlap with pathologies of premature aging. Moreover, SIRT6knockout mouse cells have genomic instability and DNA damagehypersensitivity. In biochemical fractionation assays, SIRT6 proteinassociates preferentially with a chromatin-enriched cellular fraction.Together, these observations suggested that SIRT6 might couple chromatinregulation with DNA repair. However, a physiologic role for SIRT6 insuch a process has not yet been demonstrated.

Mammalian sirtuins (SIRT1-7), homologs of the yeast Sir2, have recentlybeen proposed to be involved in the control of critical metabolicpathways as well as apoptosis, stress responses, DNA repair, cell cycle,genomic stability and gene expression. Sirtuins, also designated classIII histone deacetylases, are protein deacetylases/ADPribosyltransferases. These enzymes are highly conserved from prokaryotesto eukaryotes. They all share a conserved NAD-dependent catalytic coredomain, and exhibit variable N-terminal and C-terminal extensions thatcontribute to their unique subcellular localization and may alsoregulate their catalytic activity. The subcellular distribution,substrate specificity and cellular function of sirtuins are quitediverse. SIRT2 is a predominantly cytoplasmic protein, SIRT3-5 aremitochondrial and SIRT7, -6 and -7 are localized in the nucleus. SIRT7,the most closely related to yeast Sir2 and the best characterizedsirtuin, possesses a large number of substrates, including p53, Ku70,NF-κB and forkhead transcription factors, that regulate cellularoxidative and genotoxic stresses. SIRT6 is involved in importantfunctions in preserving cells from genomic instability and progeroidphenotype. Moreover, SIRT6 is the only sirtuin to exhibit a robustauto-ADP-ribosyltransferase activity. SIRT7 is the only sirtuinlocalized in nucleoli. It was shown to exhibit no deacetylase orADP-ribosyltansferase activity when tested on acetylated histones andvarious acetylated components of the RNA Pol I machinery. Concerning thenucleolar function of SIRT7, Ford et al. proposed that SIRT7 could be apositive regulator of rDNA transcription via its association with RNAPol I. Its overexpression enhances rDNA transcription, whereas itsinhibition reduces rDNA transcription. Interestingly, expression ofSIRT7 is positively correlated with cell growth: SIRT7 is abundant inmetabolically active tissues such as liver, spleen and tests. To date,there are no data concerning the cell cycle regulation of SIRT7 and itsfate during mitosis when rDNA transcription is repressed.

In some embodiments, antisense oligonucleotides are used to prevent ortreat diseases or disorders associated with Sirtuin (SIRT) familymembers. Exemplary Sirtuin (SIRT) mediated diseases and disorders whichcan be treated with cell/tissues regenerated from stem cells obtainedusing the antisense compounds comprise: a disease or disorder associatedwith abnormal function and/or expression of Sirtuin, cancer (e.g.,breast cancer, colorectal cancer, CCL, CML, prostate cancer), aneurodegenerative disease or disorder (e.g., Alzheimer's Disease (AD),Huntington's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis(ALS), Multiple Sclerosis, and disorders caused by polyglutamineaggregation), a beta-amyloid disease or disorder (e.g., a disordercharacterized by .beta.-amyloid accumulation such as Alzheimer'sdisease), skeletal muscle disease (e.g., Duchene muscular dystrophy,skeletal muscle atrophy, Becker's dystrophy, or myotonic dystrophy); ametabolic disease or disorder (e.g., insulin resistance, diabetes, type2 diabetes, obesity, impaired glucose tolerance, metabolic syndrome,adult-onset diabetes, diabetic nephropathy, hyperglycemia, diabeticnephropathy, Hypercholesterolemia, dyslipidemia hyperlipidemia and anage-related metabolic disease etc.), a disease or disorder associatedwith impaired insulin regulation, neuropathy (e.g., sensory neuropathy,autonomic neuropathy, motor neuropathy, retinopathy), a disease ordisorder associated with a ketogenic condition, a disease or disorderassociated with impaired energy homeostasis, a disease or disorderassociated with impaired Acetyl-CoA synthetase 2 activity, a disease ordisorder associated with metabolic homeostasis, a lipid metabolismdisease or disorder, a disease or disorder associated with impairedthermogenesis, a disease or disorder associated with impaired regulationof cell division, a disease or disorder associated with mitochondrialdysfunction, neuropathy (e.g., sensory neuropathy, autonomic neuropathy,motor neuropathy, retinopathy), fibrosis, inflammatory cardiomyopathy,heart hypertrophy, Ichronic inflammation, atherosclerosis, arthritis,dementia, osteoporosis, and a cardiovascular disease or disorder, ahepatic disease or disorder (e.g., due to alcohol abuse or hepatitis,fatty liver disease etc.), age-related macular degeneration, bonedisease (e.g., osteoporosis), a blood disease (e.g., a leukemia), boneresorption, age-related macular degeneration, AIDS related dementia,ALS, Bell's Palsy, atherosclerosis, a cardiac disease or disorder (e.g.,cardiac dysrhymias, chronic congestive heart failure, ischemic stroke,coronary artery disease and cardiomyopathy), chronically degenerativedisease (e.g., cardiac muscle disease), chronic renal failure, type 2diabetes, ulceration, cataract, presbiopia, glomerulonephritis,Guillan-Barre syndrome, hemorrhagic stroke, rheumatoid arthritis,inflammatory bowel disease, SLE, Crohn's disease, osteoarthritis,osteoporosis. Chronic Obstructive Pulmonary Disease (COPD), pneumonia,skin aging, a skin disease or disorder, urinary incontinence, a diseaseor disorder associated with mitochondrial dysfunction (e.g.,mitochondrial myopathy, encephalopathy, Leber's disease, Leighencephalopathia, Pearson's disease, lactic acidosis, ‘mitochondrialencephalopathy, lactic acidosis and stroke like symptoms’ (MELAS) etc.),liver degeneration, skeletal muscle degeneration, a muscular disease ordisorder, inflammation, a disease or disorder associated with ectopiclipid storage, a disease or disorder associated with oxidative stress, adisease or disorder associated with cellular stress, a disease ordisorder associated with neuronal cell death, aging or other conditioncharacterized by unwanted cell loss, degenerative syndrome, a disease ordisorder associated with ammonia detoxification, aging, a disease ordisorder associated with telomere dysfunction, a disease or disorderassociated with impaired chromatin regulation, a disease or disorderassociated with premature cellular senescence, a disease or disorderassociated with impared SIRT mediated DNA repair and a conditioncharacterized by unwanted cell loss.

Sirtuins have been reported to regulate TNF-alpha activity, as describedin, e.g., U.S. Pat. App. Pub. No. 2010/0137345, “Prophylactic andtherapeutic use of sirtuin inhibitors in TNF-alpha mediatedpathologies,” incorporated herein by reference in its entirety. Inembodiments antisense oligonucleotides of the present invention are usedto modulate Sirtuins, e.g., SIRT 6, to treat TNP-alpha-mediateddisorders or diseases. TNF-alpha-mediated disorders or diseases include,e.g., ankylosing spondylitis, atherosclerosis, inflammatory boweldisease (IBD) including Crohn's disease and ulcerative colitis,psoriasis, psoriatic arthritis, or rheumatoid arthritis, cachexia,Gram-negative sepsis, endotoxin-induced shock, septic shock syndrome,systemic inflammatory response syndrome (SIRS) or multiple organdysfunction syndrome (MODS); and/or graft versus host pathologies,including graft versus host disease (GVHD) and rejection of transplantedxenogenic or allogeneic tissues or organs; and/or acute or chronicinfectious or parasitic processes, including viral, bacterial or fungal,infections and protozoan or metazoan parasite infections, preferablycerebral malaria or meningococcal meningitis; and/or allergic disorders,including allergic rhinitis, allergic conjunctivitis, asthma, eczema,urticaria, contact dermatitis, systemic allergic response (anaphylaxis)and anaphylactic shock, allergic rhinitis or asthma, acute disseminatedencephalomyelitis (ADEM); Addison's disease; ankylosing spondylitis;antiphospholipid antibody syndrome (APS); aplastic anemia;atherosclerosis; autoimmune gastritis; autoimmune hepatitis; autoimmunethrombocytopenia; Behcet's disease; coeliac disease; dermatomyositis;diabetes mellitus type I; diabetes mellitus type II; familialMediterranean fever; familial cold-induced autoinflammatory syndrome;Goodpasture's syndrome; gout; pseudogout; Graves' disease;Guillain-Barre syndrome (GBS); Hashimoto's disease; hereditary periodicfevers; idiopathic thrombocytopenic purpura; inflammatory bowel disease(IBD) including Crohn's disease and ulcerative colitis;ischemia-reperfusion injury; Kawasaki's disease; mixed connective tissuedisease; Muckle-Wells syndrome; multiple sclerosis (MS); myastheniagravis; opsoclonus myoclonus syndrome (OMS); optic neuritis; Ord'sthyroiditis; osteoarthritis; pemphigus; pernicious anaemia;polyarteritis nodosa; polymyositis; postoperative or traumaticinflammation; primary biliary cirrhosis; primary myoxedema; psoriasis;psoriatic arthritis; rheumatic fever; rheumatoid arthritis; Reiter'ssyndrome; scleroderma; Sjogren's syndrome; stroke-ischemia; systemiclupus erythematosus (SLE); systemic onset juvenile idiopathic arthritis;Takayasu's arteritis; temporal arteritis; vitiligo; warm autoimmunehemolytic anemia; and Wegener's granulomatosis.

In another embodiment, the antisense oligonucleotides modulate thenormal expression and/or normal function of a Sirtuin (SIRT) in patientssuffering from or at risk of developing diseases or disorders associatedwith Sirtuin (SIRT).

In embodiments of the present invention, therapeutic and/or cosmeticregimes and related tailored treatments are provided to subjectsrequiring skin treatments or at risk of developing conditions for whichthey would require skin treatments. Diagnosis can be made, e.g., basedon the subject's SIRT status. A patient's SIRT expression levels in agiven tissue such as skin can be determined by methods known to those ofskill in the art and described elsewhere herein, e.g., by analyzingtissue using PCR or antibody-based detection methods.

A preferred embodiment of the present invention provides a compositionfor skin treatment and/or a cosmetic application comprising SIRTantisense oligonucleotides, e.g., to upregulate expression of SIRT inthe skin. Examples of antisense oligonucleotides are set forth as SEQ IDNOS: 24 to 127. U.S. Pat. No. 7,544,497, “Compositions for manipulatingthe lifespan and stress response of cells and organisms,” incorporatedherein by reference, describes potential cosmetic use for agents thatmodulate Sirtuin activity by reducing the K_(m) of the Sirtuin proteinfor its substrate. In embodiments, cells are treated in vivo with theoligonucleotides of the present invention, to increase cell lifespan orprevent apoptosis. For example, skin can be protected from aging, e.g.,developing wrinkles, by treating skin, e.g., epithelial cells, asdescribed herein. In an exemplary embodiment, skin is contacted with apharmaceutical or cosmetic composition comprising a SIRT antisensecompound as described herein. Exemplary skin afflictions or skinconditions include disorders or diseases associated with or caused byinflammation, sun damage or natural aging. For example, the compositionsfind utility in the prevention or treatment of contact dermatitis(including irritant contact dermatitis and allergic contact dermatitis),atopic dermatitis (also known as allergic eczema), actinic keratosis,keratinization disorders (including eczema), epidermolysis bullosadiseases (including penfigus), exfoliative dermatitis, seborrheicdermatitis, erythemas (including erythema multiforme and erythemanodosum), damage caused by the sun or other light sources, discoid lupuserythematosus, dermatomyositis, skin cancer and the effects of naturalaging.

Sirtuin has been reported to interfere with dihydrotestosterone-inducedandrogen receptor signaling. (See, e.g., Fu, et al., 2006, “HormonalControl of Androgen Receptor Function through SIRT1,” Molecular andCellular Biology 26(21): 8122-8135, incorporated herein by reference.)In embodiments of the present invention, a composition comprising SIRTantisense oligonucleotides, e.g., to upregulate expression of SIRT inthe scalp and inhibit androgen receptor signaling, thereby preventingandrogenetic alopecia (hair loss). In embodiments, a patient sufferingfrom alopecia is administered either a topical or systemic formulation.In an embodiment, an antisense oligonucleotide described herein isincorporated into a topical formulation containing a topical carrierthat is generally suited to topical drug administration and comprisingany such material known in the art. The topical carrier may be selectedso as to provide the composition in the desired form, e.g., as anointment, lotion, cream, microemulsion, gel, oil, solution, or the like,and may be comprised of a material of either naturally occurring orsynthetic origin. It is preferable that the selected carrier notadversely affect the active agent or other components of the topicalformulation. Examples of suitable topical carriers for use hereininclude water, alcohols and other nontoxic organic solvents, glycerin,mineral oil, silicone, petroleum jelly, lanolin, fatty acids, vegetableoils, parabens, waxes, and the like. Formulations may be colorless,odorless ointments, lotions, creams, microemulsions and gels.

Antisense oligonucleotides of the invention may be incorporated intoointments, which generally are semisolid preparations which aretypically based on petrolatum or other petroleum derivatives. Thespecific ointment base to be used, as will be appreciated by thoseskilled in the art, is one that will provide for optimum drug delivery,and, preferably, will provide for other desired characteristics as welle.g., emolliency or the like. As with other carriers or vehicles, anointment base should be inert, stable, nonirritating and nonsensitizing.As explained in Remington's Pharmaceutical Sciences (Mack Pub. Co.),ointment bases may be grouped into four classes: oleaginous bases;emulsifiable bases; emulsion bases; and water-soluble bases. Oleaginousointment bases include, for example, vegetable oils, fats obtained fromanimals, and semisolid hydrocarbons obtained from petroleum.Emulsifiable ointment bases, also known as absorbent ointment bases,contain little or no water and include, for example, hydroxystearinsulfate, anhydrous lanolin and hydrophilic petrolatum. Emulsion ointmentbases are either water-in-oil (W/O) emulsions or oil-in-water (O/W)emulsions, and include, for example, cetyl alcohol, glycerylmonostearate, lanolin and stearic acid. Exemplary water-soluble ointmentbases are prepared from polyethylene glycols (PEGs) of varying molecularweight (see, e.g., Remington's, supra).

Antisense oligonucleotides of the invention may be incorporated intolotions, which generally are preparations to be applied to the skinsurface without friction, and are typically liquid or semiliquidpreparations in which solid particles, including the active agent, arepresent in a water or alcohol base. Lotions are usually suspensions ofsolids, and may comprise a liquid oily emulsion of the oil-in-watertype. Lotions are preferred formulations for treating large body areas,because of the case of applying a more fluid composition. It isgenerally necessary that the insoluble matter in a lotion be finelydivided. Lotions will typically contain suspending agents to producebetter dispersions as well as compounds useful for localizing andholding the active agent in contact with the skin, e.g.,methylcellulose, sodium carboxymethylcellulose, or the like. Anexemplary lotion formulation for use in conjunction with the presentmethod contains propylene glycol mixed with a hydrophilic petrolatumsuch as that which may be obtained under the trademark Aquaphor® fromBeiersdorf, Inc. (Norwalk, Conn.).

Antisense oligonucleotides of the invention may be incorporated intocreams, which generally are viscous liquid or semisolid emulsions,either oil-in-water or water-in-oil. Cream bases are water-washable, andcontain an oil phase, an emulsifier and an aqueous phase. The oil phaseis generally comprised of petrolatum and a fatty alcohol such as cetylor stearyl alcohol; the aqueous phase usually, although not necessarily,exceeds the oil phase in volume, and generally contains a humectant. Theemulsifier in a cream formulation as explained in Remington's, supra, isgenerally a nonionic, anionic, cationic or amphoteric surfactant.

Antisense oligonucleotides of the invention may be incorporated intomicroemulsions, which generally are thermodynamically stable,isotropically clear dispersions of two immiscible liquids, such as oiland water, stabilized by an interfacial film of surfactant molecules(Encyclopedia of Pharmaceutical Technology (New York: Marcel Dekker,1992), volume 9). For the preparation of microemulsions, surfactant(emulsifier), co-surfactant (co-emulsifier), an oil phase and a waterphase are necessary. Suitable surfactants include any surfactants thatare useful in the preparation of emulsions, e.g., emulsifiers that aretypically used in the preparation of creams. The co-surfactant (or“co-emulsifier”) is generally selected from the group of polyglycerolderivatives, glycerol derivatives and fatty alcohols. Preferredemulsifier/co-emulsifier combinations are generally although notnecessarily selected from the group consisting of: glyceryl monostearateand polyoxyethylene stearate; polyethylene glycol and ethylene glycolpalmitostearate; and caprilic and capric triglycerides and oleoylmacrogolglycerides. The water phase includes not only water but also,typically, buffers, glucose, propylene glycol, polyethylene glycols,preferably lower molecular weight polyethylene glycols (e.g., PEG 300and PEG 400), and/or glycerol, and the like, while the oil phase willgenerally comprise, for example, fatty acid esters, modified vegetableoils, silicone oils, mixtures of mono- di- and triglycerides, mono anddi-esters of PEG (e.g., oleoyl macrogol glycerides), etc.

Antisense oligonucleotides of the invention may be incorporated into gelformulations, which generally are semisolid systems consisting of eithersuspensions made up of small inorganic particles (two-phase systems) orlarge organic molecules distributed substantially uniformly throughout acarrier liquid (single phase gels). Single phase gels can be made, forexample, by combining the active agent, a carrier liquid and a suitablegelling agent such as tragacanth (at 2 to 5%), sodium alginate (at2-10%), gelatin (at 2-15%), methylcellulose (at 3-5%), sodiumcarboxymethylcellulose (at 2-5%), carbomer (at 0.3-5%) or polyvinylalcohol (at 10-20%) together and mixing until a characteristic semisolidproduct is produced. Other suitable gelling agents, includemethylhydroxycellulose, polyoxyethylene-polyoxypropylene,hydroxyethylcellulose and gelatin. Although gels commonly employ aqueouscarrier liquid, alcohols and oils can be used as the carrier liquid aswell.

Various additives, known to those skilled in the art, may be included informulations, e.g., topical formulations. Examples of additives include,but are not limited to, solubilizers, skin permeation enhancers,opacifiers, preservatives (e.g., anti-oxidants), gelling agents,buffering agents, surfactants (particularly nonionic and amphotericsurfactants), emulsifiers, emollients, thickening agents, stabilizers,humectants, colorants, fragrance, and the like. Inclusion ofsolubilizers and/or skin permeation enhancers is particularly preferred,along with emulsifiers, emollients and preservatives. An optimum topicalformulation comprises approximately: 2 wt. % to 60 wt. %, preferably 2wt. % to 50 wt. % solubilizer and/or skin permeation enhancer; 2 wt. %to 50 wt. %, preferably 2 wt. % to 20 wt. %, emulsifiers; 2 wt. % to 20wt. % emollient; and 0.01 to 0.2 wt. % preservative, with the activeagent and carrier (e.g., water) making of the remainder of theformulation.

A skin permeation enhancer serves to facilitate passage of therapeuticlevels of active agent to pass through a reasonably sized area ofunbroken skin. Suitable enhancers are well known in the art and include,for example: lower alkanols such as methanol ethanol and 2-propanol;alkyl methyl sulfoxides such as dimethylsulfoxide (DMSO),decylmethylsulfoxide (C.sub.10 MSO) and tetradecylmethyl sulfboxide;pyrrolidones such as 2-pyrrolidone, N-methyl-2-pyrrolidone andN-(-hydroxyethyl)pyrrolidone; urea; N,N-diethyl-m-toluamide;C.sub.2-C.sub.6 alkanediols; miscellaneous solvents such as dimethylformamide (DMF), N,N-dimethylactamide (DNA) and tetrahydrofurfurylalcohol; and the 1-substituted azacycloheptan-2-ones, particularly1-n-dodecylcyclazacycloheptan-2-one (laurocapram; available under thetrademark Azone® from Whitby Research Incorporated, Richmond, Va.).

Examples of solubilizers include, but are not limited to, the following:hydrophilic ethers such as diethylene glycol monoethyl ether(ethoxydiglycol, available commercially as Transcutol®) and diethyleneglycol monoethyl ether oleate (available commercially as Soficutol®);polyethylene castor oil derivatives such as polyoxy 35 castor oil,polyoxy 40 hydrogenated castor oil, etc.; polyethylene glycol,particularly lower molecular weight polyethylene glycols such as PEG 300and PEG 400, and polyethylene glycol derivatives such as PEG-8caprylic/capric glycerides (available commercially as Labrasol®); alkylmethyl sulfoxides such as DMSO; pyrrolidones such as 2-pyrrolidone andN-methyl-2-pyrrolidone; and DMA. Many solubilizers can also act asabsorption enhancers. A single solubilizer may be incorporated into theformulation, or a mixture of solubilizers may be incorporated therein.

Suitable emulsifiers and co-emulsifiers include, without limitation,those emulsifiers and co-emulsifiers described with respect tomicroemulsion formulations. Emollients include, for example, propyleneglycol, glycerol, isopropyl myristate, polypropylene glycol-2 (PPG-2)myristyl ether propionate, and the like.

Other active agents may also be included in formulations, e.g., otheranti-inflammatory agents, analgesics, antimicrobial agents, antifungalagents, antibiotics, vitamins, antioxidants, and sunblock agentscommonly found in sunscreen formulations including, but not limited to,anthranilates, benzophenones (particularly benzophenone-3), camphorderivatives, cinnamates (e.g., octyl methoxycinnamate), dibenzoylmethanes (e.g., butyl methoxydibenzoyl methane), p-aminobenzoic acid(PABA) and derivatives thereof, and salicylates (e.g., octylsalicylate).

In one embodiment, the oligonucleotides are specific for polynucleotidesof a Sirtuin (SIRT), which includes, without limitation noncodingregions. The Sirtuin (SIRT) targets comprise variants of a Sirtuin(SIRT); mutants of a Sirtuin (SIRT), including SNPs; noncoding sequencesof a Sirtuin (SIRT); alleles, fragments and the like. Preferably theoligonucleotide is an antisense RNA molecule.

In accordance with embodiments of the invention, the target nucleic acidmolecule is not limited to Sirtuin (SIRT) polynucleotides alone butextends to any of the isoforms, receptors, homologs, non-coding regionsand the like of a Sirtuin (SIRT).

In another embodiment, an oligonucleotide targets a natural antisensesequence (natural antisense to the coding and non-coding regions) of aSirtuin (SIRT) targets, including, without limitation, variants,alleles, homology mutants, derivatives, fragments and complementarysequences thereto. Preferably the oligonucleotide is an antisense RNA orDNA molecule.

In another embodiment, the oligomeric compounds of the present inventionalso include variants in which a different base is present at one ormore of the nucleotide positions in the compound. For example, if thefirst nucleotide is an adenine, variants may be produced which containthymidine, guanosine, cytidine or other natural or unnatural nucleotidesat this position. This may be done at any of the positions of theantisense compound.

In some embodiments, homology, sequence identity or complementarity,between the antisense compound and target is from about 50% to about60%. In some embodiments, homology, sequence identity orcomplementarity, is from about 60% to about 70%. In some embodiments,homology, sequence identity or complementarity, is from about 70% toabout 80%. In some embodiments, homology, sequence identity orcomplementarity, is from about 80% to about 90%. In some embodiments,homology, sequence identity or complementarity, is about 90%, about 92%,about 94%, about 95%, about 96%, about 97%, about 98%, about 99% orabout 100%.

An antisense compound is specifically hybridizable when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a loss of activity, and there is asufficient degree of complementarity to avoid non-specific binding ofthe antisense compound to non-target nucleic acid sequences underconditions in which specific binding is desired. Such conditionsinclude, i.e., physiological conditions in the case of in vivo assays ortherapeutic treatment, and conditions in which assays are performed inthe case of in vitro assays.

An antisense compound, whether DNA, RNA, chimeric, substituted etc, isspecifically hybridizable when binding of the compound to the target DNAor RNA molecule interferes with the normal function of the target DNA orRNA to cause a loss of utility, and there is a sufficient degree ofcomplementarity to avoid non-specific binding of the antisense compoundto non-target sequences under conditions in which specific binding isdesired, i.e., under physiological conditions in the case of in vivoassays or therapeutic treatment, and in the case of in vitro assays,under conditions in which the assays are performed.

In another embodiment, targeting of a Sirtuin (SIRT) including withoutlimitation, antisense sequences which are identified and expanded, usingfor example, PCR, hybridization etc., one or more of the sequences setforth as SEQ ID NO: 9 to 23, 141 to 143, and the like, modulate theexpression or function of a Sirtuin (SIRT). in one embodiment,expression or function is up-regulated as compared to a control. Inanother embodiment, expression or function is down-regulated as comparedto a control.

In another embodiment, oligonucleotides comprise nucleic acid sequencesset forth, as SEQ ID NOS: 24to 127 including antisense sequences whichare identified and expanded, using for example, PCR, hybridization, etc.These oligonucleotides can comprise one or more modified nucleotides,shorter or longer fragments, modified bonds and the like. Examples ofmodified bonds or internucleotide linkages comprise phosphorothioate,phosphorodithioate or the like. In another embodiment, the nucleotidescomprise a phosphorus derivative. The phosphorus derivative (or modifiedphosphate group) which may be attached to the sugar or sugar analogmoiety in the modified oligonucleotides of the present invention may bea monophosphate, diphosphate, triphosphate, alkylphosphate,alkanephosphate, phosphorothioate and the like. The preparation of theabove-noted phosphate analogs, and their incorporation into nucleotides,modified nucleotides and oligonucleotides, per se, is also known andneed not be described here.

The specificity and sensitivity of antisense is also harnessed by thoseof skill in the art for therapeutic uses. Antisense oligonucleotideshave been employed as therapeutic moieties in the treatment of diseasestates in animals and man. Antisense oligonucleotides have been safelyand effectively administered to humans and numerous clinical trials arepresently underway. It is thus established that oligonucleotides can beuseful therapeutic modalities that can be configured to be useful intreatment regimes for treatment of cells, tissues and animals,especially humans.

In embodiments of the present invention oligomeric antisense compounds,particularly oligonucleotides, bind to target nucleic acid molecules andmodulate the expression and/or function of molecules encoded by a targetgene. The functions of DNA to be interfered comprise, for example,replication and transcription. The functions of RNA to be interferedcomprise all vital functions such as, for example, translocation of theRNA to the site of protein translation, translation of protein from theRNA, splicing of the RNA to yield one or more mRNA species, andcatalytic activity which may be engaged in or facilitated by the RNA.The functions may be unregulated or inhibited depending on the functionsdesired.

The antisense compounds, include, antisense oligomeric compounds,antisense oligonucleotides, external guide sequence (EGS)oligonucleotides, alternate splicers, primers, probes, and otheroligomeric compounds that hybridize to at least a portion of the targetnucleic acid. As such, these compounds may be introduced in the form ofsingle-stranded, double-stranded, partially single-stranded, or circularoligomeric compounds.

Targeting an antisense compound to a particular nucleic acid molecule,in the context of this invention, can be a multistep process. Theprocess usually begins with the identification of a target nucleic acidwhose function is to be modulated. This target nucleic acid may be, forexample, a cellular gene (or mRNA transcribed from the gene) whoseexpression is associated with a particular disorder or disease state, ora nucleic acid molecule from an infectious agent. In the presentinvention, the target nucleic acid encodes a Sirtuin (SIRT).

The targeting process usually also includes determination of at leastone target region, segment, or site within the target nucleic acid forthe antisense interaction, to occur such that the desired effect, e.g.,modulation of expression, will result. Within the context of the presentinvention, the term “region” is defined as a portion of the targetnucleic acid having at least one identifiable structure, function, orcharacteristic. Within regions of target nucleic acids are segments.“Segments” are defined as smaller or sub-portions of regions within atarget nucleic acid. “Sites,” as used in the present invention, aredefined as positions within a target nucleic acid.

In one embodiment, the antisense oligonucleotides bind to the naturalantisense sequences of a Sirtuin (SIRT) and modulate the expressionand/or function of a Sirtuin (SIRT) (SEQ ID NO: 1 to 23 and 133 to 143).Examples of antisense sequences include SEQ ID NOS: 24 to 127.

In another embodiment, the antisense oligonucleotides bind to one ormore segments of a Sirtuin (SIRT) polynucleotide and modulate theexpression and/or function of a Sirtuin (SIRT). The segments comprise atleast five consecutive nucleotides of a Sirtuin (SIRT) sense orantisense polynucleotides.

In another embodiment, the antisense oligonucleotides are specific fornatural antisense sequences of a Sirtuin (SIRT) wherein binding of theoligonucleotides to the natural antisense sequences of a Sirtuin (SIRT)modulate expression and/or function of a Sirtuin (SIRT).

In another embodiment, oligonucleotide compounds comprise sequences setforth as SEQ ID NOS: 24 to 127, antisense sequences which are identifiedand expanded, using for example, PCR, hybridization, etc. Theseoligonucleotides can comprise one or more modified nucleotides, shorteror longer fragments, modified bonds and the like. Examples of modifiedbonds or internucleotide linkages comprise phosphorothioate,phosphorodithioate or the like. In another embodiment, the nucleotidescomprise a phosphorus derivative. The phosphorus derivative (or modifiedphosphate group) which may be attached to the sugar or sugar analogmoiety in the modified oligonucleotides of the present invention may bea monophosphate, diphosphate, triphosphate, alkylphosphate,alkanephosphate, phosphorothioate and the like. The preparation of theabove-noted phosphate analogs, and their incorporation into nucleotides,modified nucleotides and oligonucleotides, per se, is also known andneed not be described here.

Since, as is known in the art, the translation initiation codon istypically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in thecorresponding DNA molecule), the translation initiation codon is alsoreferred to as the “AUG codon,” the “start codon” or the “AUG startcodon”. A minority of genes has a translation initiation codon havingthe RNA sequence 5′-GUG, 5′-UUG or 5′-CUG; and 5′-AUA, 5′-ACG and 5′-CUGhave been shown to function in vivo. Thus, the terms “translationinitiation codon” and “start codon” can encompass many codon sequences,even though the initiator amino acid in each instance is typicallymethionine (in eukaryotes) or formylmethionine (in prokaryotes).Eukaryotic and prokaryotic genes may have two or more alternative startcodons, any one of which may be preferentially utilized for translationinitiation in a particular cell type or tissue, or under a particularset of conditions. In the context of the invention, “start codon” and“translation initiation codon” refer to the codon or codons that areused in vivo to initiate translation of an mRNA transcribed from a geneencoding a Sirtuin (SIRT), regardless of the sequence(s) of such codons.A translation termination codon (or “stop codon”) of a gene may have oneof three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (the correspondingDNA sequences are 5′-TAA, 5′-TAG and 5′-TGA, respectively).

The terms “start codon region” and “translation initiation codon region”refer to a portion of such an mRNA or gene that, encompasses from about25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or3′) from a translation initiation codon. Similarly, the terms “stopcodon region” and “translation termination codon region” refer to aportion of such an mRNA or gene that encompasses from about 25 to about50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from atranslation termination codon. Consequently, the “start codon region”(or “translation initiation codon region”) and the “stop codon region”(or “translation termination codon region”) are all regions that may betargeted effectively with the antisense compounds of the presentinvention.

The open reading frame (ORF) or “coding region,” which is known in theart to refer to the region between the translation initiation codon andthe translation termination codon, is also a region which may betargeted effectively. Within the context of the present invention, atargeted region is the intragenic region encompassing the translationinitiation or termination codon of the open reading frame (ORF) of agene.

Another target region includes the 5′ untranslated region (5′UTR), knownin the art to refer to the portion of an mRNA in the 5′ direction fromthe translation initiation codon, and thus including nucleotides betweenthe 5′ cap site and the translation initiation codon of an mRNA (orcorresponding nucleotides on the gene). Still another target regionincludes the 3′ untranslated region (3′UTR), known in the art to referto the portion of an mRNA in the 3′ direction from the translationtermination codon, and thus including nucleotides between thetranslation termination codon and 3′ end of an mRNA (or correspondingnucleotides on the gene). The 5′ cap site of an mRNA comprises anN7-methylated guanosine residue joined to the 5′-most residue of themRNA via a 5′-5′ triphosphate linkage. The 5′ cap region of an mRNA isconsidered to include the 5′ cap structure itself as well as the first50 nucleotides adjacent to the cap site. Another target region for thisinvention is the 5′ cap region.

Other target regions of SIRT1 comprise nucleotides 65 to 85, and 221 to253 of the antisense transcript CV396200. In embodiments, methods ofmodulating a function of and/or expression of a SIRT1 polynucleotidecomprise contacting cells or tissues with at least one antisenseoligonucleotide that targets one or more of these regions, in part or inwhole. In certain embodiments, a combination of antisenseoligonucleotides that target one or more of these regions, and one ormore antisense transcripts that target other Sirtuins, are used. Inembodiments, multiple antisense oligonucleotides targeting differentregions of a SIRT are used in combination, or multiple antisenseoligonucleotides targeting one or more different Sirtuins areadministered in combination.

Although some eukaryotic mRNA transcripts are directly translated, manycontain one or more regions, known as “introns,” which are excised froma transcript before it is translated. The remaining (and thereforetranslated) regions are known as “exons” and are spliced together toform a continuous mRNA sequence. In one embodiment, targeting splicesites, i.e., intron-exon junctions or exon-intron junctions, isparticularly useful in situations where aberrant splicing is implicatedin disease, or where an overproduction of a particular splice product isimplicated in disease. An aberrant fusion junction due to rearrangementor deletion is another embodiment of a target site. mRNA transcriptsproduced via the process of splicing of two (or more) mRNAs fromdifferent gene sources are known as “fusion transcripts”. Introns can beeffectively targeted using antisense compounds targeted to, for example,DNA or pre-mRNA.

In another embodiment, the antisense oligonucleotides bind to codingand/or non-coding regions of a target polynucleotide and modulate theexpression and/or function of the target molecule.

In another embodiment, the antisense oligonucleotides bind to naturalantisense polynucleotides and modulate the expression and/or function ofthe target molecule.

In another embodiment, the antisense oligonucleotides bind to sensepolynucleotides and modulate the expression and/or function of thetarget molecule.

Alternative RNA transcripts can be produced from the same genomic regionof DNA. These alternative transcripts are generally known as “variants”.More specifically, “pre-mRNA variants” are transcripts produced from thesame genomic DNA that differ from other transcripts produced from thesame genomic DNA in either their start or stop position and contain bothintronic and exonic sequence.

Upon excision of one or more exon or intron regions, or portions thereofduring splicing, pre-mRNA variants produce smaller “mRNA variants”.Consequently, mRNA variants are processed pre-mRNA variants and eachunique pre-mRNA variant must always produce a unique mRNA variant as aresult of splicing. These mRNA variants are also known as “alternativesplice variants”. If no splicing of the pre-mRNA variant occurs then thepre-mRNA variant is identical to the mRNA variant.

Variants can be produced through the use of alternative signals to startor stop transcription. Pre-mRNAs and mRNAs can possess more than onestart codon or stop codon. Variants that originate from a pre-mRNA ormRNA that use alternative start codons are known as “alternative startvariants” of that pre-mRNA or mRNA. Those transcripts that use analternative stop codon are known as “alternative stop variants” of thatpre-mRNA or mRNA. One specific type of alternative stop variant is the“polyA variant” in which the multiple transcripts produced result fromthe alternative selection of one of the “polyA stop signals” by thetranscription machinery, thereby producing transcripts that terminate atunique polyA sites. Within the context of the invention, the types ofvariants described herein are also embodiments of target nucleic acids.

The locations on the target nucleic acid to which the antisensecompounds hybridize are defined as at least a 5-nucleotide long portionof a target region to which an active antisense compound is targeted.

While the specific sequences of certain exemplary target segments areset forth herein, one of skill in the art will recognize that theseserve to illustrate and describe particular embodiments within the scopeof the present invention. Additional target segments are readilyidentifiable by one having ordinary skill in the art in view of thisdisclosure.

Target segments 5-100 nucleotides in length comprising a stretch of atleast five (5) consecutive nucleotides selected from within theillustrative target segments are considered to be suitable for targetingas well.

Target segments can include DNA or RNA sequences that comprise at leastthe 5 consecutive nucleotides from the 5′-terminus of one of theillustrative target segments (the remaining nucleotides being aconsecutive stretch of she same DNA or RNA beginning immediatelyupstream of the 5′-terminus of the target segment and continuing untilthe DNA or RNA contains about 5 to about 100 nucleotides). Similarlytarget segments are represented by DNA or RNA sequences that comprise atleast the 5 consecutive nucleotides from the 3′-terminus of one of theillustrative target segments (the remaining nucleotides being aconsecutive stretch of the same DNA or RNA beginning immediatelydownstream of the 3′-terminus of the target segment and continuing untilthe DNA or RNA contains about 5 to about 100 nucleotides). One havingskill in the art armed with the target segments illustrated herein willbe able, without undue experimentation, to identify further targetsegments.

Once one or more target regions, segments or sites have been identified,antisense compounds are chosen which are sufficiently complementary tothe target, i.e., hybridize sufficiently well and with sufficientspecificity, to give the desired effect.

In embodiments of the invention the oligonucleotides bind to anantisense strand of a particular target. The oligonucleotides are atleast 5 nucleotides in length and can be synthesized so eacholigonucleotide targets overlapping sequences such that oligonucleotidesare synthesized to cover the entire length of the target polynucleotide.The targets also include coding as well as non coding regions.

In one embodiment, specific nucleic acids are targeted by antisenseoligonucleotides. Targeting an antisense compound to a particularnucleic acid, is a multistep process. The process usually begins withthe identification of a nucleic acid sequence whose function is to bemodulated. This may be, for example, a cellular gene (or mRNAtranscribed from the gene) whose expression is associated with aparticular disorder or disease state, or a non coding polynucleotidesuch as for example, non coding RNA (mRNA).

RNAs can be classified into (1) messenger RNAs (mRNAs), which aretranslated into proteins, and (2) non-protein-coding RNAs (ncRNAs).ncRNAs comprise microRNAs, antisense transcripts and otherTranscriptional Units (TU) containing a high density of stop codons andlacking any extensive “Open Reading Frame”. Many ncRNAs appear to startfrom initiation sites in 3′ untranslated regions (3′UTRs) ofprotein-coding loci. ncRNAs are often rare and at least half of thencRNAs that have been sequenced by the FANTOM consortium seem not to bepolyadenylated. Most researchers have for obvious reasons focused onpolyadenylated mRNAs that are processed and exported to the cytoplasm.Recently, it was shown that the set of non-polyadenylated nuclear RNAsmay be very large, and that many such transcripts arise from intergenicregions. The mechanism by which ncRNAs may regulate gene expression isby base pairing with target transcripts. The RNAs that function by basepairing can be grouped into (1) cis encoded RNAs that are encoded at thesame genetic location, but on the opposite strand to the RNAs they actupon and therefore display perfect complementarity to their target, and(2) trans-encoded RNAs that are encoded at a chromosomal locationdistinct from the RNAs they act upon and generally do not exhibitperfect base-pairing potential with their targets.

Without wishing to be bound by theory, perturbation of an antisensepolynucleotide by the antisense oligonucleotides described herein canalter the expression of the corresponding sense messenger RNAs. However,this regulation can either be discordant (antisense knockdown results inmessenger RNA elevation) or concordant (antisense knockdown results inconcomitant messenger RNA reduction). In these cases, antisenseoligonucleotides can be targeted to overlapping or non-overlapping partsof the antisense transcript resulting in its knockdown or sequestration.Coding as well as non-coding antisense can be targeted in an identicalmanner and that either category is capable of regulating thecorresponding sense transcripts—either in a concordant or disconcordantmanner. The strategies that are employed in identifying newoligonucleotides for use against a target can be based on the knockdownof antisense RNA transcripts by antisense oligonucleotides or any othermeans of modulating the desired target.

Strategy 1: In the case of discordant regulation, knocking down theantisense transcript elevates the expression of the conventional (sense)gene. Should that latter gene encode for a known or putative drugtarget, then knockdown of its antisense counterpart could conceivablymimic the action of a receptor agonist or an enzyme stimulant.

Strategy 2: In the case of concordant regulation, one couldconcomitantly knock down both antisense and sense transcripts andthereby achieve synergistic reduction of the conventional (sense) geneexpression. If for example, at antisense oligonucleotide is used toachieve knockdown, then this strategy can be used to apply one antisenseoligonucleotide targeted to the sense transcript and another antisenseoligonucleotide to the corresponding antisense transcript, or a singleenergetically symmetric antisense oligonucleotide that simultaneouslytargets overlapping sense and antisense transcripts.

According to the present invention, antisense compounds includeantisense oligonucleotides, ribozymes, external guide sequence (EGS)oligonucleotides, siRNA compounds, single- or double-stranded RNAinterference (RNAi) compounds such as siRNA compounds, and otheroligomeric compounds which hybridize to at least a portion of the targetnucleic acid and modulate its function. As such, they may be DNA, RNA,DNA-like, RNA-like, or mixtures thereof, or may be mimetics of one ormore of these. These compounds may be single-stranded, doublestranded,circular or hairpin oligomeric compounds and may contain structuralelements such as internal or terminal bulges, mismatches or loops.Antisense compounds are routinely prepared linearly but can be joined orotherwise prepared to be circular and/or branched. Antisense compoundscan include constructs such as, for example, two strands hybridized toform a wholly or partially double-stranded compound or a single strandwith sufficient self-complementarity to allow for hybridization andformation of a fully or partially double-stranded compound. The twostrands can be linked internally leaving free 3′ or 5′ termini or can belinked to form a continuous hairpin structure or loop. The hairpinstructure may contain an overhang on either the 5′ or 3′ terminusproducing an extension of single stranded character. The double strandedcompounds optionally can include overhangs on the ends. Furthermodifications can include conjugate groups attached to one of thetermini, selected nucleotide positions, sugar positions or to one of theinternucleoside linkages. Alternatively, the two strands can be linkedvia a non-nucleic acid moiety or linker group. When formed from only onestrand, dsRNA can take the form of a self-complementary hairpin-typemolecule that doubles back on itself to form a duplex. Thus, the dsRNAscan be fully or partially double stranded. Specific modulation of geneexpression can be achieved by stable expression of dsRNA hairpins intransgenic cell lines, however, in some embodiments, the gene expressionor function is up regulated. When formed from two strands, or a singlestrand that takes the form of a self-complementary hairpin-type moleculedoubled back on itself to form a duplex, the two stands (orduplex-forming regions of a single strand) are complementary RNA strandsthat base pair in Watson-Crick fashion.

Once introduced to a system, the compounds of the invention may elicitthe action of one or more enzymes or structural proteins to effectcleavage or other modification of the target nucleic acid or may workvia occupancy-based mechanisms. In general, nucleic acids (includingoligonucleotides) may be described as “DNA-like” (i.e., generally havingone or more 2′-deoxy sugars and, generally, T rather than U bases) or“RNA-like” (i.e., generally having one or more 2′-hydroxyl or2′-modified sugars and, generally U rather than T bases). Nucleic acidhelices can adopt more than one type of structure, most commonly the A-and B-forms. It is believed that, in general, oligonucleotides whichhave B-form-like structure are “DNA-like” and those which haveA-formlike structure are “RNA-like.” In some (chimeric) embodiments, anantisense compound may contain both A- and B-form regions.

In another embodiment, the desired oligonucleotides or antisensecompounds, comprise at least one of: antisense RNA, antisense DNA,chimeric antisense oligonucleotides, antisense oligonucleotidescomprising modified linkages, interference RNA (RNAi), short interferingRNA (siRNA); a micro, interfering RNA (miRNA); a small, temporal RNA(stRNA); or a short, hairpin RNA (shRNA); small RNA-induced geneactivation (RNAs); small activating RNAs (saRNAs), or combinationsthereof.

dsRNA can also activate gene expression, a mechanism that has beentermed “small RNA-induced gene activation” or RNAa. dsRNAs targetinggene promoters induce potent transcriptional activation of associatedgenes. RNAa was demonstrated in human cells using synthetic dsRNAs,termed “small activating RNAs” (saRNAs).

Small double-stranded RNA (dsRNA), such as small interfering RNA (siRNA)and microRNA (miRNA) have been found to be the trigger of anevolutionary conserved mechanism known as RNA interference (RNAi), RNAiinvariably leads to gene silencing. However, in instances described indetail in the examples section which follows, oligonucleotides are shownto increase the expression and/or function of the Sirtuin (SIRT)polynucleotides and encoded products thereof. dsRNAs may also act assmall activating RNAs (saRNA). Without wishing to be bound by theory, bytargeting sequences in gene promoters, saRNAs would induce target geneexpression in a phenomenon referred to as dsRNA-induced transcriptionalactivation (RNAa).

In a further embodiment, the “target segments” identified herein may beemployed in a screen for additional compounds that modulate theexpression of a Sirtuin (SIRT) polynucleotide. “Modulators” are thosecompounds that decrease or increase the expression of a nucleic acidmolecule encoding a Sirtuin (SIRT) and which comprise at least a5-nucleotide portion that is complementary to a target segment. Thescreening method comprises the steps of contacting a target segment of anucleic acid molecule encoding sense or natural antisensepolynucleotides of a Sirtuin (SIRT) with one or more candidatemodulators, and selecting for one or more candidate modulators whichdecrease or increase the expression of a nucleic acid molecule encodinga Sirtuin (SIRT) polynucleotide, e.g. SEQ ID NOS: 24 to 127. Once it isshown that the candidate modulator or modulators are capable ofmodulating (e.g. either decreasing or increasing) the expression of anucleic acid molecule encoding a Sirtuin (SIRT) polynucleotide, themodulator may then be employed in further investigative studies of thefunction of a Sirtuin (SIRT) polynucleotide, or for use as a research,diagnostic, or therapeutic agent in accordance with the presentinvention.

Targeting the natural antisense sequence modulates the function of thetarget gene. For example, the Sirtuin (SIRT) (e.g. accession numbersNM_(—)12238.4, NM_(—)001159589, NM_(—)012237.3, NM_(—)012239,NM_(—)012240, NM_(—)012241, NM_(—)016539, NM_(—)016538,NM_(—)101142498.1, NM_(—)030593.2, NM_(—)001193286.1, NR_(—)034146.1,NM_(—)001017524.2, NM_(—)031244.2, NM_(—)001193267.1,NM_(—)001193285.1). In an embodiment, the target, is an antisensepolynucleotide of the Sirtuin (SIRT). In an embodiment, an antisenseoligonucleotide targets sense and/or natural antisense sequences of aSirtuin (SIRT) polynucleotide (e.g. accession numbers NM_(—)012238.4,NM_(—)001159589. NM_(—)012237.3, NM_(—)012239, NM_(—)012240,NM_(—)012241, NM_(—)016539, NM_(—)016538, NM_(—)001142498.1,NM_(—)030593.2, NM_(—)00193286.1, NR_(—)034146.1, NM_(—)001017524.2,NM_(—)031244.2, NM_(—)001193267.1, NM_(—)001193285.1), variants,alleles, isoforms, homologs, mutants, derivatives, fragments andcomplementary sequences thereto. Preferably the oligonucleotide is anantisense molecule and the targets include coding and noncoding regionsof antisense and/or sense Sirtuin (SIRT) polynucleotides.

The target segments of the present invention may be also be combinedwith their respective complementary antisense compounds of the presentinvention to form stabilized double-stranded (duplexed)oligonucleotides.

Such double stranded oligonucleotide moieties have been shown in the artto modulate target expression and regulate translation as well as RNAprocessing via an antisense mechanism. Moreover, the double-strandedmoieties may be subject to chemical modifications. For example, suchdoable-stranded moieties have been shown to inhibit the target by theclassical hybridization of antisense strand of the duplex to the target,thereby triggering enzymatic degradation of the target.

In an embodiment, an antisense oligonucleotide targets Sirtuin (SIRT)polynucleotides (e.g. accession numbers NM_(—)012238.4, NM_(—)00159589,NM_(—)012237.3, NM_(—)012239, NM012240, NM_(—)012241, NM_(—)016539,NM_(—)016538, NM_(—)001142498.1, NM_(—)030593.2, NM_(—)00193286.1,NR034146.1, NM_(—)001017524.2, NM_(—)031244.2, NM_(—)001193267.1,NM_(—)001193285.1), variants, alleles, isoforms, homologs, mutants,derivatives, fragments and complementary sequences thereto. Preferablythe oligonucleotide is an antisense molecule.

In accordance with embodiments of the invention, the target nucleic acidmolecule is not limited to Sirtuin (SIRT) alone but extends to any ofthe isoforms, receptors, homologs and the like of a Sirtuin (SIRT)molecule.

In another embodiment, an oligonucleotide targets a natural antisensesequence of a Sirtuin (SIRT) polynucleotide, for example,polynucleotides set forth as SEQ ID NO: 9 to 23, 141 to 143, and anyvariants, alleles, homologs, mutants, derivatives, fragments andcomplementary sequences thereto. Examples of antisense oligonucleotidesare set forth as SEQ ID NOS: 24 to 127.

In one embodiment, the oligonucleotides are complementary to or bind tonucleic acid sequences of a Sirtuin (SIRT) antisense, including withoutlimitation noncoding sense and/or antisense sequences associated with aSirtuin (SIRT) polynucleotide and modulate expression and/or function ofa Sirtuin (SIRT) molecule.

In another embodiment, the oligonucleotides are complementary to or bindto nucleic acid sequences of a Sirtuin (SIRT) natural antisense, setforth as SEQ ID NO: 9 to 23, 141 to 143 and modulate expression and/orfunction of a Sirtuin (SIRT) molecule.

In an embodiment, oligonucleotides comprise sequences of at least 5consecutive nucleotides of SEQ ID NOS: 24 to 127 and modulate expressionand/or function of a Sirtuin (SIRT) molecule.

The polynucleotide targets comprise Sirtuin (SIRT), including familymembers thereof, variants of a Sirtuin (SIRT): mutants of a Sirtuin(SIRT), including SNPs: noncoding sequences of a Sirtuin (SIRT); allelesof a Sirtuin (SIRT); species variants, fragments and the like.Preferably the oligonucleotide is an antisense molecule.

In another embodiment, the oligonucleotide targeting Sirtuin (SIRT)polynucleotides, comprise: antisense RNA, interference RNA (RNAi), shortinterfering RNA (siRNA); micro interfering RNA (tmRNA); a small,temporal RNA (stRNA); or a short, hairpin RNA (shRNA); small RNA-inducedgene activation (RNAa); or, small activating RNA (saRNA).

In another embodiment, targeting of a Sirtuin (SIRT) polynucleotide,e.g. SEQ ID NO: 9 to 23, 141 to 143 modulate the expression or functionof these targets. In one embodiment, expression or function isupregulated as compared to a control. In another embodiment, expressionor function is down-regulated as compared to a control.

In another embodiment, antisense compounds comprise sequences set forthas SEQ ID NOS: 24 to 127. These oligonucleotides can comprise one ormore modified nucleotides, shorter or longer fragments, modified bondsand the like.

In another embodiment, SEQ ID NOS: 24 to 127 comprise one or more LNAnucleotides.

The modulation of a desired target nucleic acid can be carried out inseveral ways known in the art, for example, antisense oligonucleotides,siRNA etc. Enzymatic nucleic acid molecules (e.g., ribozymes) arenucleic acid molecules capable of catalyzing one or more of a variety ofreactions, including the ability to repeatedly cleave other separatenucleic acid molecules in a nucleotide base sequence-specific manner.Such enzymatic nucleic acid molecules can be used, for example, totarget virtually any RNA transcript.

Because of their sequence-specificity, trans-cleaving enzymatic nucleicacid molecules show promise as therapeutic agents for human disease.Enzymatic nucleic acid molecules can be designed to cleave specific RNAtargets within the background of cellular RNA. Such a cleavage eventraiders the mRNA non-functional and abrogates protein expression fromthat RNA. In this manner, synthesis of a protein associated with adisease state can be selectively inhibited.

In general, enzymatic nucleic acids with RNA cleaving activity act byfirst binding to a target RNA. Such binding occurs through the targetbinding portion of a enzymatic nucleic acid which is held in closeproximity to an enzymatic portion of the molecule that acts to cleavethe target RNA. Thus, the enzymatic nucleic acid first recognizes andthen binds a target RNA through complementary base pairing, and oncebound to the correct site, acts enzymatically to cut the target RNA.Strategic cleavage of such a target RNA will destroy its ability todirect synthesis of an encoded protein. After an enzymatic nucleic acidhas bound and cleaved its RNA target, it is released from that RNA tosearch for another target and can repeatedly bind and cleave newtargets.

Several approaches such as in vitro selection (evolution) strategieshave been used to evolve new nucleic acid catalysts capable ofcatalyzing a variety of reactions, such as cleavage and ligation ofphosphodiester linkages and amide linkages.

The development of ribozymes that are optimal for catalytic activitywould contribute significantly to any strategy that employs RNA-cleavingribozymes for the purpose of regulating gene expression. The hammerheadribozyme, for example, functions with a catalytic rate (kcat) of about 1min-l in the presence of saturating (10 mM) concentrations of Mg2+cofactor. An artificial “RNA ligase” ribozyme has been shown to catalyzethe corresponding self-modification reaction with a rate of about 100min-l. In addition, it is known that certain modified hammerheadribozymes that have substrate binding arms made of DNA catalyze RNAcleavage with multiple turn-over rates that approach 100 min-l. Finally,replacement of a specific residue within the catalytic core of thehammerhead with certain nucleotide analogues gives modified ribozymesthat show as much as a 10-fold improvement in catalytic rate. Thesefindings demonstrate that ribozymes can promote chemical transformationswith catalytic rates that are significantly greater than those displayedin vitro by most natural, self-cleaving ribozymes. It is then possiblethat the structures of certain selfcleaving ribozymes may be optimizedto give maximal catalytic activity, or that entirely new RNA motifs canbe made that display significantly faster rates for RNA phosphodiestercleavage.

Intermolecular cleavage of an RNA substrate by an RNA catalyst that fitsthe “hammerhead” model was first shown in 1987. The RNA catalyst wasrecovered and reacted with multiple RNA molecules, demonstrating that itwas truly catalytic.

Catalytic RNAs designed based on the “hammerhead” motif have been usedto cleave specific target sequences by snaking appropriate base changesin the catalytic RNA to maintain necessary base pairing with the targetsequences. This has allowed use of the catalytic RNA to cleave specifictarget sequences and indicates that catalytic RNAs designed according tothe “hammerhead” model may possibly cleave specific substrate RNAs invivo.

RNA interference (RNAi) has become a powerful tool for modulating geneexpression in mammals and mammalian cells. This approach requires thedelivery of small interfering RNA (siRNA) either as RNA itself or asDNA, using an expression plasmid or virus and the coding sequence forsmall hairpin RNAs that are processed to siRNAs. This system enablesefficient transport of the pre-siRNAs to the cytoplasm where they areactive and permit the use of regulated and tissue specific promoters forgene expression.

In one embodiment, an oligonucleotide or antisense compound comprises anoligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleicacid (DNA), or a mimetic, chimera, analog or homolog thereof. This termincludes oligonucleotides composed of naturally occurring nucleotides,sugars and covalent internucleoside (backbone) linkages as well asoligonucleotides having non-naturally occurring portions which functionsimilarly. Such modified or substituted oligonucleotides are oftendesired over native forms because of desirable properties such as, forexample, enhanced cellular uptake, enhanced affinity for a targetnucleic acid and increased stability in the presence of nucleases.

According to the present invention, the oligonucleotides or “antisensecompounds” include antisense oligonucleotides (e.g. RNA, DNA, mimetic,chimera, analog or homolog thereof), ribozymes, external guide sequence(EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNAinterference (RNAi) compounds such as siRNA compounds, saRNA, aRNA, andother oligomeric compounds which hybridize to at least a portion of thetarget nucleic acid and modulate its function. As such, they may be DNA,RNA, DNA-like, RNA-like, or mixtures thereof, or may be mimetics of oneor more of these. These compounds may be single-stranded,double-stranded, circular or hairpin oligomeric compounds and maycontain structural elements such as internal or terminal bulges,mismatches or loops. Antisense compounds are routinely prepared linearlybut can be joined or otherwise prepared to be circular and/or branched.Antisense compounds can include constructs such as, for example, twostrands hybridized to form a wholly or partially double-strandedcompound or a single strand with sufficient self-complementarity toallow for hybridization and formation of a fully or partiallydouble-stranded compound. The two strands can be linked internallyleaving free 3′or 5′ termini or can be linked to form a continuoushairpin structure or loop. The hairpin structure may contain an overhangon either the 5′ or 3′ terminus producing an extension of singlestranded character. The double stranded compounds optionally can includeoverhangs on the ends. Further modifications can include conjugategroups attached to one of the termini, selected nucleotide positions,sugar positions or to one of the internucleoside linkages.Alternatively, the two strands can be linked via a non-nucleic acidmoiety or linker group. When formed from only one strand, dsRNA can takethe form of a self-complementary hairpin-type molecule that doubles backon itself to form a duplex. Thus, the dsRNAs can be fully or partiallydouble stranded. Specific modulation of gene expression can be achievedby stable expression of dsRNA hairpins in transgenic cell lines. Whenformed from two strands, or a single strand that takes the form of aself-complementary hairpin-type molecule doubled back on itself to forma duplex, the two strands (or duplex-forming regions of a single strand)are complementary RNA strands that base pair in Watson-Crick fashion.

Once introduced to a system, the compounds of the invention may elicitthe action of one or more enzymes or structural proteins to effectcleavage or other modification of the target nucleic acid or may workvia occupancy-based mechanisms. In general, nucleic acids (includingoligonucleotides) may be described as “DNA-like” (i.e., generally havingone or more 2′-deoxy sugars and, generally, T rather than U bases) or“RNA-like” (i.e., generally having one or more 2′-hydroxyl or2′-modified sugars and, generally U rather than T bases). Nucleic acidhelices can adopt more than one type of structure, most commonly the A-and B-forms. It is believed that, in general, oligonucleotides whichhave B-form-like structure are “DNA-like” and those which haveA-formlike structure are “RNA-like.” In some (chimeric) embodiments, anantisense compound may contain both A- and B-form regions.

The antisense compounds in accordance with this invention can comprisean antisense portion from about 5 to about 80 nucleotides (i.e. fromabout 5 to about 80 linked nucleosides) in length. This refers to thelength of the antisense strand or portion of the antisense compound. Inother words, a single-stranded antisense compound of the inventioncomprises front 5 to about 80 nucleotides, and a double-strandedantisense compound of the invention (such as a dsRNA, for example)comprises a sense and an antisense strand or portion of 5 to about 80nucleotides in length. One of ordinary skill in the art will appreciatethat this comprehends antisense portions of 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides inlength, or any range therewithin.

In one embodiment, the antisense compounds of the invention haveantisense portions of 10 to 50 nucleotides in length. One havingordinary skill in the art will appreciate that this embodiesoligonucleotides having antisense portions of 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50nucleotides in length, or any range therewithin. In some embodiments,the oligonucleotides are 15 nucleotides in length.

In one embodiment, the antisense or oligonucleotide compounds of theinvention have antisense portions of 12 or 13 to 30 nucleotides inlength. One having ordinary skill in the art will appreciate that thisembodies antisense compounds having antisense portions of 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30nucleotides in length, or any range therewithin.

In another embodiment, the oligomeric compounds of the present inventionalso include variants in which a different base is present at one ormore of the nucleotide positions in the compound. For example, if thefirst nucleotide is an adenosine, variants may be produced which containthymidine, guauosine or cytidine at this position. This may be done atany of the positions of the antisense or dsRNA compounds. Thesecompounds are then tested using the methods described herein todetermine their ability to inhibit expression of a target nucleic acid.

In some embodiments, homology, sequence identity or complementarity,between the antisense compound and target is from about 40% to about60%. In some embodiments, homology, sequence identity orcomplementarity, is from about 60% to about 70%. In some embodiments,homology, sequence identity or complementarity, is from about 70% toabout 80%. In some embodiments, homology, sequence identity orcomplementarity, is from about 80% to about 90%. In some embodiments,homology, sequence identity or complementarity, is about 90%, about 92%,about 94%, about 95%, about 96%, about 97%, about 98%, about 99% orabout 100%.

In another embodiment, the antisense oligonucleotides, such as forexample, nucleic acid molecules set forth in SEQ ID NOS: 24 to 127comprise one or more substitutions or modifications. In one embodiment,the nucleotides are substituted with locked nucleic acids (LNA).

In another embodiment, the oligonucleotides target one or more regionsof the nucleic acid molecules sense and/or antisense of coding and/ornon-coding sequences associated with SIRT and the sequences set forth asSEQ ID NOS: 1 to 23 and 133 to 143. The oligonucleotides are alsotargeted to overlapping regions of SEQ ID NOS: 1 to 23 and 133 to 143.

Certain oligonucleotides of this invention are chimericoligonucleotides. “Chimeric oligonucleotides” or “chimeras,” in thecontext of this invention, are oligonucleotides which contain two ormore chemically distinct regions, each made up of at least onenucleotide. These oligonucleotides typically contain at least one regionof modified nucleotides that confers one or more beneficial properties(such as, for example, increased nuclease resistance, increased uptakeinto cells, increased binding affinity for the target) and a region thatis a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNAhybrids. By way of example, RNase H is a cellular endonuclease whichcleaves the RNA strand of an RNA/DNA duplex. Activation of RNase H,therefore, results in cleavage of the RNA target, thereby greatlyenhancing the efficiency of antisense modulation of gene expression.Consequently, comparable results can often be obtained with shorteroligonucleotides when chimeric oligonucleotides are used, compared tophosphorothioate deoxyoligonucleotides hybridizing to the same targetregion. Cleavage of the RNA target can be routinely detected by gelelectrophoresis and, if necessary, associated nucleic acid hybridizationtechniques known in the art. In one embodiment, a chimericoligonucleotide comprises at least one region modified to increasetarget binding affinity, and, usually, a region that acts as a substratefor RNAse H. Affinity of an oligonucleotide for its target (in thiscase, a nucleic acid encoding ras) is routinely determined by measuringthe Tm of an oligonucleotide/target pair, which is the temperature atwhich the oligonucleotide and target dissociate; dissociation isdetected spectrophotometrically. The higher the Tm, the greater is theaffinity of the oligonucleotide for the target.

Chimeric antisense compounds of the invention may be formed as compositestructures of two or more oligonucleotides, modified oligonucleotides,oligonucleosides and/or oligonucleotides mimetics as described above.Such; compounds have also been referred to in the art as hybrids orgapmers. Representative United States patents that teach the preparationof such, hybrid structures comprise, but are not limited to, U.S. Pat.Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922,each of which is herein incorporated by reference.

In another embodiment, the region of the oligonucleotide which ismodified comprises at least one nucleotide modified at the 2′ positionof the sugar, most preferably a 2′-O-alkyl, 2′-O-alkyl-O-alkyl or2′-fluoro-modified nucleotide. In other embodiments, RNA modificationsinclude 2′-fluoro, 2′-amino and 2′ O-methyl modifications on the riboseof pyrimidines, abasic residues or an inverted base at the 3″ end of theRNA. Such modifications are routinely incorporated into oligonucleotidesand these oligonucleotides have been shown to have a higher Tm (i.e.,higher target binding affinity) than; 2′-deoxyoligonucleotides against agiven target. The effect of such increased affinity is to greatlyenhance RNAi oligonucleotide inhibition of gene expression. RNAse H is acellular endonuclease that cleaves the RNA strand of RNA:DNA duplexes;activation of this enzyme therefore results in cleavage of the RNAtarget, and thus can greatly enhance the efficiency of RNAi inhibition.Cleavage of the RNA target can be routinely demonstrated by gelelectrophoresis. In another embodiment, the chimeric oligonucleotide isalso modified to enhance nuclease resistance. Cells contain a variety ofexo and endo-nucleases which can degrade nucleic acids. A number ofnucleotide and nucleoside modifications have been shown to make theoligonucleotide into which they are incorporated more resistant tonuclease digestion than the native oligodeoxynucleotide. Nucleaseresistance is routinely measured by incubating oligonucleotides withcellular extracts or isolated nuclease solutions and measuring theextent of intact oligonucleotide remaining over time, usually by gelelectrophoresis. Oligonucleotides which have been modified to enhancetheir nuclease resistance survive intact for a longer time thanunmodified oligonucleotides. A variety of oligonucleotide modificationshave been demonstrated to enhance or confer nuclease resistance.Oligonucleotides which contain at least one phosphorothioatemodification are presently more preferred. In some eases,oligonucleotide modifications which enhance target binding affinity arealso, independently, able to enhance nuclease resistance. Some desirablemodifications can be found in De Mesmaeker et al. (1995) Acc. Chem.Res., 28:366-374.

Specific examples of some oligonucleotides envisioned for this inventioninclude those comprising modified backbones, for example,phosphorothioates, phosphotriesters, methyl phosphonates, short chainalkyl or cycloalkyl intersugar linkages or short chain heteroatomic orheterocyclic intersugar linkages. Most are oligonucleotides withphosphorothioate backbones and those with heteroatom backbones,particularly CH2 —NH—O—CH2, CH, —N(CH3)—O—CH2 [known as amethylene(methylimino) or MMI backbone], CH2—O—N (CH3)—CH2, CH2 —N(CH3)—N (CH3)—CH2 and O—N (CH3)—CH2 —CH2 backbones, wherein the nativephosphodiester backbone is represented as O—P—O—CH,). The amidebackbones disclosed by De Mesmaeker et al. (1995) Acc. Chem. Res.28:366-374 are also preferred. Also are oligonucleotides havingmorpholino backbone structures (Summerton and Weller, U.S. Pat. No.5,034,506). In other embodiments, such as the peptide nucleic acid (PNA)backbone, the phosphodiester backbone of the oligonucleotide is replacedwith a polyamide backbone, the nucleotides being bound directly orindirectly to the aza nitrogen atoms of the polyamide backbone.Oligonucleotides may also comprise one or more substituted sugarmoieties, oligonucleotides comprise one of the following at the 2′position: OH, SH, SCH3, F, OCN, OCH3 OCH3 OCH3 (CH2)n CH3, O(CH2)n NH2or O(CH2)n CH3 where n is from 1 to about 10; C1 to C10 lower alkyl,alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CM;CF3; OCF3; O—, S—, or N-alkyl; O—, S—, or N-alkenyl; SOCH3; SO2 CH3;ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl;aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleavinggroup; a reporter group: an intercalator; a group for improving thepharmacokinetic properties of an oligonucleotide; or a group forimproving the pharmacodynamic properties of an oligonucleotide and othersubstituents having similar properties. A modification includes2′-methoxyethoxy [2′-O—CH2 CH2 OCH3, also known as2′-O-(2-methoxyethyl)]. Other modifications include 2′-methoxy(2′-O—CH3), 2′-propoxy (2′-OCH2 CH2CH3) and 2′-fluoro (2′-F). Similarmodifications may also be made at other positions on theoligonucleotide, particularly the 3′ position of the sugar on the 3′terminal nucleotide and the 5′ position of 5′ terminal nucleotide.Oligonucleotides may also have sugar mimetics such as cyclobutyls inplace of the pentofuranosyl group.

Oligonucleotides may also include, additionally or alternatively,nucleobase (often referred to in the art simply as “base”) modificationsor substitutions. As used herein, “unmodified” or “natural” nucleotidesinclude adenine (A), guanine (G), thymine (T), cytokine (C) and uracil(U). Modified nucleotides include nucleotides found only infrequently ortransiently in natural nucleic acids, e.g., hypoxanthine,6-methyladenine, 5-Me pyrimidines, particularly 5-methylcytosine (alsoreferred to as 5-methyl-2′ deoxycytosine and often referred to in theart as 5-Me—C), 5-hydroxymethylcytosine (HMC), glycosyl HMC andgentobiosyl HMC, as well as synthetic nucleotides, e.g., 2-aminoadenine,2-(methylamino)adenine, 2-(imidazolylalkyl)adenine,2-(aminoalklyamino)adenine or other heterosubstituted alkyladenines,2-thiouracil, 2-thiothymine, 5-bromouracil, 5-hydroxymetyhluracil,8-azaguanine, 7-deazaguanine, N6 (6-aminohexyl)adenine and2,6-diaminopurine. A “universal” base known in the art, e.g., inosine,may be included. 5-Me—C substitutions have been shown to increasenucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y, S., in Crooke,S. T. and Lebleu, B., eds., Antisense Research and Applications, CRCPress, Boca Raton, 1993, pp. 276-278) and are presently basesubstitutions.

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates which enhance the activity or cellular uptake of theoligonucleotide. Such moieties include but are not limited to lipidmoieties such as a cholesterol moiety, a cholesteryl moiety, athioether, e.g., hexyl-S-trityithiol, a thiocholesterol, an aliphaticchain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid. Oligonucleotidescomprising lipophilic moieties, and methods for preparing sucholigonucleotides are known in the art, for example, U.S. Pat. Nos.5,138,045, 5,218,105 and 5,459,255.

It is not necessary for all positions in a given oligonucleotide to beuniformly modified, and in fact more than one of the aforementionedmodifications may be incorporated in a single oligonucleotide or even atwithin a single nucleoside within an oligonucleotide. The presentinvention also includes oligonucleotides which are chimericoligonucleotides as hereinbefore defined.

In another embodiment, the nucleic acid molecule of the presentinvention is conjugated with another moiety including but not limited toabasic nucleotides, polyether, polyamine, polyamides, peptides,carbohydrates, lipid, or polyhydrocarbon compounds. Those skilled in theart will recognize that these molecules can be linked to one or more ofany nucleotides comprising the nucleic acid molecule at severalpositions on the sugar, base or phosphate group.

The oligonucleotides used in accordance with this invention may beconveniently and routinely made through the well-known technique ofsolid phase synthesis. Equipment for such synthesis is sold by severalvendors including Applied Biosystems. Any other means for such synthesismay also be employed; the actual synthesis of the oligonucleotides iswell within the talents of one of ordinary skill in the art. It is alsowell known to use similar techniques to prepare other oligonucleotidessuch as the phosphorothioates and alkylated derivatives. It is also wellknown to use similar techniques and commercially available modifiedamidites and controlled-pore glass (CPG) products such as biotin,fluorescein, acridine or psoralen-modified amidites and/or CPG(available from Glen Research, Sterling Va.) to synthesize fluorescentlylabeled, biotinylated or other modified oligonucleotides such ascholesterol-modified oligonucleotides.

In accordance with the invention, use of modifications such as the useof LNA monomers to enhance the potency, specificity and duration ofaction and broaden the routes of administration of oligonucleotidescomprised of current chemistries such as MOE, ANA, FANA, PS etc. Thiscan be achieved by substituting some of the monomers in the currentoligonucleotides by LNA monomers. The LNA modified oligonucleotide mayhave a size similar to the parent compound or may be larger orpreferably smaller. It is that such LNA-modified oligonucleotidescontain less than about 70%, more preferably less man about 60%, mostpreferably less man about 50% LNA monomers and that their sizes arebetween about 5 and 25 nucleotides, more preferably between about 12 and20 nucleotides.

Modified oligonucleotide backbones comprise, but are not limited to,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl, and other alkylphosphonates comprising 3′alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates comprising 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates.thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Varioussalts, mixed salts and free acid forms are also included.

Representative United States patents that teach the preparation of theabove phosphorus containing linkages comprise, but are not limited to,U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;5,587,361; and 5,625,050, each of which is herein incorporated byreference.

Modified oligonucleotide backbones that do not include a phosphorus atomtherein have backbones that are formed by short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These comprisethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH2 component parts.

Representative United States patents that teach the preparation of theabove oligonucleotides comprise, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289;5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312;5,633,360; 5,677,437; and 5,677,439, each of which is hereinincorporated by reference.

In other oligonucleotide mimetics, both the sugar and theinternucleoside linkage, i.e., the backbone, of the nucleotide units arereplaced with novel groups. The base units are maintained forhybridization with an appropriate nucleic acid target compound. One sucholigomeric compound, an oligonucleotide mimetic that has been shown tohave excellent hybridization properties, is referred to as a peptidenucleic acid (PNA). In PNA compounds, the sugar-backbone of anoligonucleotide is replaced with an amide containing backbone, inparticular an aminoethylglycine backbone. The nucleobases are retainedand are bound directly or indirectly to aza nitrogen atoms of the amideportion of the backbone. Representative United States patents that teachthe preparation of PNA compounds comprise, bat are not limited to, U.S.Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference. Further teaching of PNA compounds can befound in Nielsen et al. (1991) Science 254, 1497-1500.

In another embodiment of the invention the oligonucleotides withphosphorothioate backbones and oligonucleosides wife heteroatombackbones, and in particular-CH2—NH—O—CH2—,—CH2—N (CH3)—O—CH2-known as amethylene (methylimino) or MMI backbone, —CH2—O—N(CH3)—CH2—,—CH2(CH3)—N(CH3) CH2-and-O—N(CH3)—CH2—CH2— wherein the nativephosphodiester backbone is represented as-O—P—O—CH2— of the abovereferenced U.S. Pat. No. 5,489,677, and the amide backbones of the abovereferenced U.S. Pat. No. 5,602,240. Also are oligonucleotides havingmorpholino backbone structures of the above-referenced U.S. Pat. No.5,034,506.

Modified oligonucleotides may also contain one or more substituted sugarmoieties, oligonucleotides comprise one of the following at the 2′position: OH; F; O—, S—, or N-alkyl; O—, or N-alkenyl; O—, S— orN-alkynyl; or O alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynylmay be substituted or unsubstituted C to CO alkyl or C2 to CO alkenyland alkynyl. Particularly are O (CH2)n OmCH3, O(CH2)n,OCH3, O(CH2)nNH2,O(CH2)nCH3, O(CH2)nONH2, and O(CH2nON(CH2)nCH3)2 where n and m can befrom 1 to about 10. Other oligonucleotides comprise one of the followingat the 2′ position; C to CO, (lower alkyl, substituted lower alkyl,alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN,CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl,heterocyoloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl,an RNA cleaving group, a reporter group, an intercalator, a group forimproving the pharmacokinetic properties of an oligonucleotide, or agroup for improving the pharmacodynamic properties of anoligonucleotide, and other substituents having similar properties. Amodification comprises 2′-methoxyethoxy (2′-O-CH2CH2OCH3, also known as2′—O—(2-methoxyethyl) or 2′-MOE) i.e., an alkoxyalkoxy group. A furthermodification comprises 2′-dimethylaminooxyethoxy, i.e., aO(CH2)2ON(CH3)2 group, also known as 2′-DMAOE, as described in examplesherein below, and 2′-dimethylaminoethoxyethoxy (also known in the art as2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e., 2′—O—CH2—O—CH2—N(CH2)2.

Other modifications comprise 2′-methoxy (2′—O CH3), 2′-aminopropoxy(2′—O CH2CH2CH2NH2) and 2′-fluoro (2′—F). Similar modifications may alsobe made at other positions on the oligonucleotide, particularly the 3′position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linkedoligonucleotides and the 5′ position of 5′ terminal nucleotide.Oligonucleotides may also have sugar mimetics such as cyclobutylmoieties in place of the pentofuranosyl sugar. Representative UnitedStates patents that teach the preparation of such modified sugarstructures comprise, but are not limited to, U.S. Pat. Nos. 4,981,957;5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786;5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909;5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and5,700,920, each of which is herein incorporated by reference.

Oligonucleotides may also comprise nucleobase (often referred to in theart simply as “base”) modifications or substitutions. As used herein,“unmodified” or “natural” nucleotides comprise the purine bases adenine(A) and guanine (CO, and the pyrimidine bases thymine (T), cytosine (C)and uracil (U). Modified nucleotides comprise other synthetic andnatural nucleotides such as 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and otheralkyl derivatives of adenine and guanine, 2-propyl and other alkylderivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil andcytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudo-uracil),4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl andother 8-substituted adenines and guanines, 5-halo particularly 5-bromo,5-trifluoromethyl and other 5-substituted uracils and cytosines,7-methylquanine and 7-methyladenine, 8-azaguanine and 8-azaadenine,7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Further, nucleotides comprise those disclosed in U.S. Pat. No.3,687,808, those disclosed in ‘The Concise Encyclopedia of PolymerScience And Engineering’, pages 858-859, Kroschwitz, J. I., ed. JohnWiley & Sons, 1990, those disclosed by Engisch et al., ‘AngewandleChemie, International Edition’, 1991, 30, page 613, and those disclosed,by Sanghvi, Y. S., Chapter 15, ‘Antisense Research and Applications’,pages 289-302, Crooke, S. T. and. Lebleu, B. ea., CRC Press, 1993.Certain of these nucleotides are particularly useful for increasing thebinding affinity of the oligomeric compounds of the invention. Thesecomprise 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and0-6 substituted purines, comprising 2-aminopropyladenine,5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutionshave been shown to increase nucleic acid duplex stability by 0.6-1.2°C.(Sanghvi, Y. S., Crooks, S. T. and Lebleu. B., eds, ‘Antisense Researchand Applications’, CRC Press, Boca Raton, 1993, pp. 276-278) and arepresently base substitutions, even more particularly when combined with2′-Omethoxyethyl sugar modifications.

Representative United States patents that teach the preparation of theabove noted modified nucleotides as well as other modified nucleotidescomprise, but are not limited to, U.S. Pat. No. 3,687,808, as well asU.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066;5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711;5,552,540; 5,587,469; 5,596,091; 5,614,617; 5,750,692, and 5,681,941,each of which is herein incorporated by reference.

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates, which enhance the activity, cellular distribution, orcellular uptake of the oligonucleotide.

Such moieties comprise but are not limited to, lipid moieties such as acholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol,a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecylresidues, a phospholipid, e.g., di-hexadecyl-rac-glycerol ortriethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, apolyamine or a polyethylene glycol chain, or adamantane acetic acid, apalmityl moiety, or an octadecylamine or hexylamino-carbonyl-toxycholesterol moiety.

Representative United States patents that teach the preparation of sucholigonucleotides conjugates comprise, but are not limited to, U.S. Pat.Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, each of whichis herein incorporated by reference.

Drug discovery: The compounds of the present invention can also beapplied in the areas of drug discovery and target validation. Thepresent invention comprehends the use of the compounds and targetsegments identified herein in drug discovery efforts to elucidaterelationships that exist between a Sirtuin (SIRT) polynucleotide and adisease state, phenotype, or condition. These methods include detectingor modulating a Sirtuin (SIRT) polynucleotide comprising contacting asample, tissue, cell, or organism with the compounds of the presentinvention, measuring the nucleic acid or protein level of a Sirtuin(SIRT) polynucleotide and/or a related phenotypic or chemical endpointat some time after treatment, and optionally comparing the measuredvalue to a non-treated sample or sample treated with a further compoundof the invention. These methods can also be performed in parallel or incombination with other experiments to determine the function of unknowngenes for the process of target validation or to determine the validityof a particular gene product as a target for treatment or prevention ofa particular disease, condition, or phenotype.

Assessing Up-Regulation or Inhibition of Gene Expression

Transfer of an exogenous nucleic acid into a host cell or organism canbe assessed by directly detecting the presence of the nucleic acid inthe cell or organism. Such detection can be achieved by several methodswell known in the art. For example, the presence of the exogenousnucleic acid can be detected by Southern blot or by a polymerase chainreaction (PCR) technique using primers that specifically amplifynucleotide sequences associated with the nucleic acid. Expression of theexogenous nucleic acids can also be measured using conventional methodsincluding gene expression analysis. For instance, mRNA produced from anexogenous nucleic acid can be detected and quantified using a Northernblot and reverse transcription PCR (RT-PCR).

Expression of RNA from the exogenous nucleic acid can also be detectedby measuring an enzymatic activity or a reporter protein activity. Forexample, antisense modulatory activity can be measured indirectly as adecrease or increase in target nucleic acid expression as an indicationthat the exogenous nucleic acid is producing the effector RNA. Based onsequence conservation, primers can be designed and used to amplifycoding regions of the target genes. Initially, the most highly expressedcoding region from each gene can be used to build a model control gene,although any coding or non coding region can be used. Each control geneis assembled by inserting each coding region between a reporter codingregion and its poly(A) signal. These plasmids would produce an mRNA witha reporter gene in the upstream portion of the gene and a potential RNAitarget in the 3′ non-coding region. The effectiveness of individualantisense oligonucleotides would be assayed by modulation of thereporter gene. Reporter genes useful in the methods of the presentinvention include acetohydroxyacid synthase (AHAS), alkaline phosphatase(AP), beta galactosidase (LacZ), beta glucoronidase (GUS),chloramphenicol acetyltransferase (CAT), green fluorescent protein(GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP),cyan fluorescent protein (CFP), horseradish peroxidase (HRP), luciferase(Luc), nopaline synthase (NOS), octopine synthase (OCS), and derivativesthereof. Multiple selectable markers are available that conferresistance to ampicillin, bleomycin, chloramphenicol, gentamycin,hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin,puromycin, and tetracycline. Methods to determine modulation of areporter gene are well known in the art, and include, but are notlimited to, flourometric methods (e.g. fluorescence spectroscopy,Fluorescence Activated Cell Sorting (FACS), fluorescence microscopy),antibiotic resistance determination.

SIRT1, SIRT3 and SIRT6 proteins and mRNA expression can be assayed usingmethods known to those of skill in the art and described elsewhereherein. For example, immunoassays such as the ELISA can be used tomeasure protein levels. Sirtuin (SIRT) antibodies for ELISAs areavailable commercially, e.g., from R&D Systems (Minneapolis, Minn.),Abcam, Cambridge, Mass.

In embodiments, SIRT1, SIRT3 and SIRT6 expression (e.g., mRNA orprotein) in a sample (e.g., cells or tissues in vivo or in vitro)treated using an antisense oligonucleotide of the invention is evaluatedby comparison with Sirtuin (SIRT) expression in a control sample. Forexample, expression of the protein or nucleic acid can be compared usingmethods known to those of skill in the art with that in a mock-treatedor untreated simple. Alternatively, comparison with a sample treatedwith a control antisense oligonucleotide (e.g., one having an altered ordifferent sequence) can be made depending on the information desired. Inanother embodiment, a difference in the expression of the Sirtuin (SIRT)protein or nucleic acid in a treated vs. an untreated sample can becompared with the difference in expression of a different nucleic acid(including any standard deemed appropriate by the researcher, e.g., ahousekeeping gene) in a treated sample vs. an untreated sample,

Observed differences can be expressed as desired, e.g., in the form of aratio or fraction, for use in a comparison with control. In embodiments,the level of a Sirtuin (SIRT) mRNA or protein, in a sample treated withan antisense oligonucleotide of the present invention, is increased ordecreased by about 1.25-fold to about 10-fold or more relative to anuntreated sample or a sample treated with a control nucleic acid. Inembodiments, the level of a Sirtuin (SIRT) mRNA or protein is increasedor decreased by at least about 1.25-fold, at least about 1.3-fold, atleast about 1.4-fold, at least about 1.5-fold, at least about 1.6-fold,at least about 1.7-fold, at least about 1.8-fold, at least about 2-fold,at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold,at least about 4-fold, at least about 4.5-fold, at least about 5-fold,at least about 5.5-fold, at least about 6-fold, at least about 6.5-fold,at least about 7-fold, at least about 7.5-fold, at least about 8-fold,at least about 8.5-fold, at least about 9-fold, at least about 9.5-fold,or at least about 10-fold or more.

Kits, Research Regents, Diagnostics, and Therapeutics

The compounds of the present invention can be utilized for diagnostics,therapeutics, and prophylaxis, and as research reagents and componentsof kits. Furthermore, antisense oligonucleotides, which are able toinhibit gene expression with exquisite specificity, are often used bythose of ordinary skill to elucidate the function of particular genes orto distinguish between functions of various members of a biologicalpathway.

For use in kits and diagnostics and in various biological systems, thecompounds of the present invention, either alone or in combination withother compounds or therapeutics, are useful as tools in differentialand/or combinatorial analyses to elucidate expression patterns of aportion or the entire complement of genes expressed within cells andtissues.

As used herein, the term “biological system” or “system” is defined asany organism, cell, cell culture or tissue that expresses, or is madecompetent to express products of the Sirtuin (SIRT). These include, butare not limited to, humans, transgenic animals, cells, cell cultures,tissues, xenografts, transplants and combinations thereof.

As one non limiting example, expression patterns within cells or tissuestreated with one or more antisense compounds are compared to controlcells or tissues not treated with antisense compounds and the patternsproduced are analyzed for differential levels of gene expression as theypertain, for example, to disease association, signaling pathway,cellular localization, expression level, size, structure or function ofthe genes examined. These analyses can be performed on stimulated orunstimulated cells and in the presence or absence of other compoundsthat affect expression patterns.

Examples of methods of gene expression analysis known in the art includeDNA arrays or microarrays. SAGE (serial analysis of gene expression),READS (restriction enzyme amplification of digested cDNAs), TOGA (totalgene expression analysis), protein arrays and proteomics, expressedsequence tag (EST) sequencing, subtractive RNA fingerprinting (SuRF),subtractive clotting, differential display (DD), comparative genomichybridization, FISH (fluorescent in situ hybridization) techniques andmass spectrometry methods.

The compounds of the invention are useful for research and diagnostics,because these compounds hybridize to nucleic acids encoding a Sirtuin(SIRT). For example, oligonucleotides that hybridize with suchefficiency and under such conditions as disclosed herein as to beeffective Sirtuin (SIRT) modulator are effective primers or probes underconditions favoring gene amplification or detection, respectively. Theseprimers and probes are useful in methods requiring the specificdetection of nucleic acid molecules encoding a Sirtuin (SIRT) and in theamplification of said nucleic acid molecules for detection or for use infurther studies of a Sirtuin (SIRT). Hybridization of the antisenseoligonucleotides, particularly the primers and probes, of the inventionwith a nucleic acid encoding a Sirtuin (SIRT) can be detected by meansknown in the art. Such means may include conjugation of an enzyme to theoligonucleotide, radiolabeling of the oligonucleotide, or any othersuitable detection means. Kits using such detection means for detectingthe level of a Sirtuin (SIRT) in a sample may also be prepared.

The specificity and sensitivity of antisense are also harnessed by thoseof skill in the art for therapeutic uses. Antisense compounds have beenemployed as therapeutic moieties in the treatment of disease states inanimals, including humans. Antisense oligonucleotide drugs have beensafely and effectively administered to humans and numerous clinicaltrials are presently underway. It is thus established that antisensecompounds can be useful therapeutic modalities that can be configured tobe useful in treatment regimes for the treatment of cells, tissues andanimals, especially humans.

For therapeutics, an animal, preferably a human, suspected of having adisease or disorder which can be treated by modulating the expression ofa Sirtuin (SIRT) polynucleotide is treated by administering antisensecompounds in accordance with this invention. For example, in onenon-limiting embodiment, the methods comprise the step of administeringto the animal in need of treatment, a therapeutically effective amountof a Sirtuin (SIRT) modulator. The Sirtuin (SIRT) modulators of thepresent invention effectively modulate the activity of a Sirtuin (SIRT)or modulate the expression of a Sirtuin (SIRT) protein. In oneembodiment, the activity or expression of a Sirtuin (SIRT) in an animalis inhibited by about 10% as compared to a control. Preferably, theactivity or expression of a Sirtuin (SIRT) in an animal is inhibited byabout 30%. More preferably, the activity or expression of a Sirtuin(SIRT) in an animal is inhibited by 50% or more. Thus, the oligomericcompounds modulate expression of a Sirtuin (SIRT) mRNA by at least 10%,by at least 50%, by at least 25%, by at least 30%, by at least 40%, byat least 50%, by at least 60%, by at least 70%, by at least 75%, by atleast 80%, by at least 85%, by at least 90%, by at least 95%, by atleast 98%, by at least 99%. or by 100% as compared to a control.

In one embodiment, the activity or expression of a Sirtuin (SIRT) and/orin an animal is increased by about 10% as compared to a control.Preferably, the activity or expression of a Sirtuin (SIRT) in an animalis increased by about 30%. More preferably, the activity or expressionof a Sirtuin (SIRT) in an animal is increased by 50% or more. Thus, theoligomeric compounds modulate expression of a Sirtuin (SIRT) mRNA by atleast 10%, by at least 50%, by at least 25%, by at least 30%, by atleast 40%, by at least 50%, by at least 60%, by at least 70%, by atleast 75%, by at least 80%, by at least 85%, by at least 90%, by atleast 95%, by at least 98%, by at least 99%, or by 100% as compared to acontrol.

In embodiments, Sirtuin modulation is observed by measuring levels ofSirtuin mRNA, antisense RNA, protein, biomarkers for Sirtuins, orcombinations thereof, in a biological sample. Sirtuin biomarkersinclude, e.g., MCP-1, BMP Receptor 1A, Smpd13a, CD14, ApoE, FAS,Transthyretin, FABP1, Acyl-CoA thioesterase 1, Acyl-CoA thioesterase 2,Aquaporin 4, Rrad, CXCL9, CCL8, Pppltr3g, ApoA-I, ApoA-II, and ApoB.Biomarkers for Sirtuin expression and their use in monitoring Sirtuinexpression is described, e.g., in U.S. Pat. App. Pub. No. 2010/0215632,“Biomarkers of Sirtuin Activity and Methods of Use Thereof,”incorporated herein by reference in its entirety.

Assays for Sirtuin activity include assays foracetyltansferase/deacetylase activity. Such assays have been describedin the literature, e.g., in U.S. Pat. App. Pub. No. 2009/0221.020, “MassSpectrometry Assays for Acetyltransferase/Deacetylase Activity,”incorporated herein by reference in its entirety. Any assay for Sirtuinactivity known to those of skill in the art is contemplated for use inmeasuring Sirtuin activity in conjunction with the methods of thepresent invention.

In certain embodiments, modulation of Sirtuin expression is identifiedby an increase in (upregulation of) or a decrease in (downregalation of)the Sirtuin mRNA copy number, mRNA concentration, or biomarker mRNA orprotein expression or activity, of at least about 10%, at least about15%, at least about 20%, at least about 25%, at least about 30%, atleast about 40%, at least about 50%, at least about 60%, at least about70%, at least about 75%, at least about 80%, at least about 90%, atleast about 100%, at least about 125%, at least about 150%, at leastabout 200%, at least about 250%, at least about 300%, at least about3500%, at least about 400%, at least about 450%, or at least about 500%,at least about 600%, at least about 700%, at least about 800%, at leastabout 900%, or at least about 1000%, in comparison to a control, e.g.,an untreated or mock-treated sample. In embodiments, the Sirtuin mRNAcopy number, mRNA concentration, or biomarker mRNA or protein expressionor activity increases or decreases by about 10% to about 500%. Inembodiments, the Sirtuin mRNA copy number, mRNA concentration, orbiomarker mRNA or protein expression or activity increases or decreasesby about 10% to about 50%, about 10% to about 100%, about 10% to about150%, about 10% to about 200%, about 10% to about 250%, about 10% toabout 300%, about 10% to about 350%, about 10% to about 400%, about 10%to about 450%, about 10% to about 500%, about 10% to about 600%, about10% to about 700%, about 10% to about 800%, about 10% to about: 900%,about 10% to about 1000%, about 50% to about 100%, about 50% to about150%, about 50% to about 200%, about 50% to about 250%,, about 50% toabout 300%, about 50% to about 350%, about 50% to about 400%, about 50%to about 450%, about 50% to about 500%, about 50% to about 600%, about50% to about 700%, about 50% to about 800%, about 50% to about 900%,about 50% to about 1000%, about 100% to about 150%, about 100% to about200%, about 100% to about 250%, about 100% to about 300%, about 100% toabout 350%, about 100% to about 400%, about 100% to about 450%, about100% to about 500%, about 100% to about 600%, about 100% to about 700%,about 100% to about 800%, about 100% to about 900%, about 100% to about1000%, about 150% to about 200%, about 150% to about 250%, about 150% toabout 300%, about 150% to about 350%, about 150% to about 400%, about150% to about 450%, about 150% to about 500%, about 150% to about 600%,about 150% to about 700%, about 150% to about 800%, about 150% to about900%, about 150% to about 1000%, about 200% to about 250%, about 200% toabout 300%, about 200% to about 350%, about 200% to about 400%, about200% to about 450%, about 200% to about 500%, about 200% to about 600%,about 200% to about 700%, about 200% to about 800%, about 200% to about900%, or about 200% to about 1000%.

For example, the reduction of the expression of a Sirtuin (SIRT) may bemeasured in serum, blood, adipose tissue, liver or any other body fluid,tissue or organ of the animal. Preferably, the cells contained withinsaid fluids, tissues or organs being analyzed contain a nucleic acidmolecule encoding Sirtuin (SIRT) peptides and/or the Sirtuin (SIRT)protein itself.

The compounds of the invention can be utilized in pharmaceuticalcompositions by adding an effective amount of a compound to a suitablepharmaceutically acceptable diluent or carrier. Use of the compounds andmethods of the invention may also be useful prophylactically.

Conjugates: Another modification of the oligonucleotides of theinvention involves chemically linking to the oligonucleotide one or moremoieties or conjugates that enhance the activity, cellular distributionor cellular uptake of the oligonucleotide. These moieties or conjugatescan include conjugate groups covalently bound to functional groups suchas primary or secondary hydroxyl groups. Conjugate groups of theinvention include intercalators, reporter molecules, polyamines,polyamides, polyethylene glycols, polyethers, groups that enhance thepharmacodynamic properties of oligomers, and groups that enhance thepharmacokinetic properties of oligomers. Typicalconjugate groups includecholesterols, lipids, phospholipids, biotin, phenazine, folate,phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines,coumarins, and dyes. Groups that enhance the pharmacodynamic properties,in the context of this invention, include groups that improve uptake,enhance resistance to degradation, and/or strengthen sequence-specifichybridization with the target nucleic acid. Groups that enhance thepharmacokinetic properties, in the context of this invention, includegroups that improve uptake, distribution, metabolism or excretion of thecompounds of the present invention. Representative conjugate groups aredisclosed in International Patent Application No. PCT/US92/09196, filedOct. 23, 1992, and U.S. Pat. No. 6,287,860, which are incorporatedherein by reference. Conjugate moieties include, but are not limited to,lipid moieties such as a cholesterol moiety, cholic acid, a thioether,e.g., hexyl-5-tritylthiol, a thiocholesterol, an aliphatic chain, e.g.,dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-Hphosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid, a palmityl moiety,or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.Oligonucleotides of the invention may also be conjugated to active drugsubstances, for example, aspirin, warfarin, phenylbutazone, ibuprofen,suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinicacid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, abarbiturate, a cephalosporin, a sulfa drug, an antidiabetic, anantibacterial or an antibiotic.

Representative United States patents that teach the preparation of sucholigonucleotide conjugates include, but are not limited to, U.S. Pat.Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941.

Formulations: The compounds of the invention may also be admixed,encapsulated, conjugated or otherwise associated with other molecules,molecule structures or mixtures of compounds, as for example. liposomes,receptor-targeted molecules, oral, rectal, topical or otherformulations, for assisting in uptake, distribution and/or absorption.Representative United States patents that teach the preparation of suchuptake, distribution and/or absorption-assisting formulations include,but are not limited to, U.S. Pat. Nos. 5,108,921; 5,354,844; 5,416,016;5,459,127; 5,521,291; 5,543,165; 5,547,932; 5,583,020; 5,591,721;4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170;5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854;5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948;5,580,575; and 5,595,756, each of which is herein incorporated byreference.

Although, the antisense oligonucleotides do not need to be administeredin the context of a vector in order to modulate a target expressionand/or function, embodiments of the invention relates to expressionvector constructs for the expression of antisense oligonucleotides,comprising promoters, hybrid promoter gene sequences and possess astrong constitutive promoter activity, or a promoter activity which canbe induced in the desired case.

In an embodiment, invention practice involves administering at least oneof the foregoing antisense oligonucleotides with a suitable nucleic aciddelivery system. In one embodiment, that system includes a non-viralvector operably linked to the polynucleotide. Examples of such nonviralvectors include the oligonucleotide alone (e.g. any one or more of SEQID NOS: 24 to 127) or in combination with a suitable protein,polysaccharide or lipid formulation.

Additionally suitable nucleic acid delivery systems include viralvector, typically sequence from at least one of an adenovirus,adenovirus-associated virus (AAV), helper-dependent adenovirus,retrovirus, or hemagglutinatin virus of Japan-liposome (HVJ) complex.Preferably, the viral vector comprises a strong eukaryotic promoteroperably linked to the polynucleotide e.g., a cytomegalovirus (CMV)promoter.

Additionally vectors include viral vectors, fusion proteins and chemicalconjugates. Retroviral vectors include Moloney murine leukemia virusesand HIV-based viruses. One HIV-based viral vector comprises at least twovectors wherein the gag and pol genes are from an HIV genome and the envgene is from another virus. DNA viral vectors are preferred. Thesevectors include pox vectors such as orthopox or avipox vectors,herpesvirus vectors such as a herpes simplex I virus (HSV) vector,Adenovirus Vectors and Adeno-associated Virus Vectors).

The antisense compounds of the invention encompass any pharmaceuticallyacceptable salts, esters, or salts of such esters, or any other compoundwhich, upon administration to an animal, including a human, is capableof providing (directly or indirectly) the biologically active metaboliteor residue thereof.

The term “pharmaceutically acceptable salts” refers to physiologicallyand pharmaceutically acceptable salts of the compounds of the invention:i.e., salts that retain the desired biological activity of the parentcompound and do not impart undesired toxicological effects thereto. Foroligonucleotides, examples of pharmaceutically acceptable salts andtheir uses are further described in U.S. Pat. No. 6,287,860, which isincorporated herein by reference.

The present invention also includes pharmaceutical compositions andformulations that include the antisense compounds of the invention. Thepharmaceutical compositions of the present invention may be administeredin a number of ways depending upon whether local or systemic treatmentis desired and upon the area to be treated. Administration may betopical (including ophthalmic and to mucous membranes including vaginaland rectal delivery), pulmonary, e.g., by inhalation or insufflation ofpowders or aerosols, including by nebulizer; intratracheal, intranasal,epidermal and transdermal), oral or parenteral. Parenteraladministration includes intravenous, intraarterial, subcutaneous,intraperitoneal or intramuscular injection or infusion; or intracranial,e.g., intrathecal or intraventricular, administration.

For treating tissues in the central nervous system, administration canbe made by, e.g., injection or infusion into the cerebrospinal fluid.Administration of antisense RNA into cerebrospinal fluid is described,e.g., in U.S. Pat App. Pub. No. 2007/0117772, “Methods for slowingfamilial ALS disease progression,” incorporated herein by reference inits entirety.

When it is intended that the antisense oligonucleotide of the presentinvention be administered to cells in the central nervous system,administration can be with one or more agents capable of promotingpenetration of the subject antisense oligonucleotide across theblood-brain barrier. Injection can be made, e.g., in the entorhinalcortex or hippocampus. Delivery of neurotrophic factors byadministration of an adenovirus vector to motor neurons in muscle tissueis described in, e.g., U.S. Pat. No. 6,632,427,“Adenoviral-vector-mediated gene transfer into medullary motor neurons,”incorporated herein by reference. Delivery of vectors directly to thebrain, e.g., the striatum, the thalamus, the hippocampus, or thesubstantia nigra, is known in the art and described, e.g., in U.S. Pat.No. 6,756,523, “Adenovirus vectors for the transfer of foreign genesinto cells of the central nervous system particularly in brain,”incorporated herein by reference. Administration can be rapid as byinjection or made over a period of time as by slow infusion oradministration of slow release formulations.

The subject antisense oligonucleotides can also be linked or conjugatedwith agents that provide desirable pharmaceutical or pharmacodynamicproperties. For example, the antisense oligonucleotide can be coupled toany substance, known in the art to promote penetration or transportacross the blood-brain barrier, such as an antibody to the transferrinreceptor, and administered by intravenous injection. The antisensecompound can be linked with a viral vector, for example, that makes theantisense compound more effective and/or increases the transport of theantisense compound across the blood-brain barrier. Osmotic blood brainbarrier disruption can also be accomplished by, e.g., infusion of sugarsincluding, but not limited to, meso erythritol, xylitol, D(+) galactose,D(+) lactose, D(+) xylose, dulcitol, myo-inositol, L(−) fructose, D(−)mannitol, D(+) glucose, D(+) arabinose, D(−) arabinose, cellobiose, D(+)maltose, D(+) raffinose, L(+) rhamnose, D(+) melibiose, D(−) ribose,adonitol, D(+) arabitol L(−) arabitol, D(+) fucose, L(−) fucose, D(−)lyxose, L(+) lyxose, and L(−) lyxose, or amino acids including, but notlimited to, glutamine, lysine, arginine, asparagine, aspartic acid,cysteine, glutamic acid, glycine, histidine, leucine, methionine,phenylalanine, proline, serine, threonine, tyrosine, valine, andtaurine. Methods and materials for enhancing blood brain barrierpenetration are described, e.g., in U.S. Pat. No. 4,866,042, “Method forthe delivery of genetic material across the blood brain barrier” U.S.Pat. No. 6,294,520, “Material for passage through the blood-brainbarrier,” and U.S. Pat. No. 6,936,589, “Parenteral delivery systems,”all incorporated herein by reference in their entirety.

The subject antisense compounds may be admixed, encapsulated, conjugatedor otherwise associated with other molecules, molecule structures ormixtures of compounds, for example, liposomes, receptor-targetedmolecules, oral, rectal, topical or other formulations, for assisting inuptake, distribution and/or absorption. For example, cationic lipids maybe included in the formulation to facilitate oligonucleotide uptake. Onesuch composition shown to facilitate uptake is LIPOFECTIN (availablefrom GIBCO-BRL, Bethesda, Md.).

Oligonucleotides with at least one 2′-O-methoxyethyl modification arebelieved to be particularly useful for oral administration.Pharmaceutical compositions and formulations for topical administrationmay include transdermal patches, ointments, lotions, creams, gels,drops, suppositories, sprays, liquids and powders. Conventionalpharmaceutical carriers, aqueous, powder or oily bases, thickeners andthe like may be necessary or desirable. Coated condoms, gloves and thelike may also be useful.

The pharmaceutical formulations of the present invention, which mayconveniently be presented in unit dosage form, may be prepared accordingto conventional techniques well known in the pharmaceutical industry.Such techniques include the step of bringing into association the activeingredients with the pharmaceutical carrier(s) or excipient(s). Ingeneral, the formulations are prepared by uniformly and intimatelybringing into association the active ingredients with liquid carriers orfinely divided solid carriers or both, and then, if necessary, shapingthe product.

The compositions of the present invention may be formulated into any ofmany possible dosage forms such as, but not limited to, tablets,capsules, gel capsules, liquid syrups, soft gels, suppositories, andenemas. The compositions of the present invention may also be formulatedas suspensions in aqueous, non-aqueous or mixed media. Aqueoussuspensions may further contain substances that increase the viscosityof the suspension including, for example, sodium carboxymethylcellulose,sorbitol and/or dextran. The suspension may also contain stabilizers.

Pharmaceutical compositions of the present invention include, but arenot limited to, solutions, emulsions, foams and liposome-containingformulations. The pharmaceutical compositions and formulations of thepresent invention may comprise one or more penetration enhancers,carriers, excipients or other active or inactive ingredients.

Emulsions are typically heterogeneous systems of one liquid dispersed inanother in the form of droplets usually exceeding 0.1 μm in diameter.Emulsions may contain additional components in addition to the dispersedphases, and the active drug that may be present as a solution in eitherthe aqueous phase, oily phase or itself as a separate phase.Microemulsions are included as an embodiment of the present invention.Emulsions and their uses are well known in the art and are furtherdescribed in U.S. Pat. No. 6,287,860.

Formulations of the present invention include liposomal formulations. Asused in the present invention, the term “liposome” means a vesiclecomposed of amphiphilic lipids arranged in a spherical bilayer orbilayers. Liposomes are unilamellar or multilamellar vesicles which havea membrane formed from a lipophilic material and an aqueous interiorthat contains the composition to be delivered. Cationic liposomes arepositively charged liposomes that are believed to interact withnegatively charged DNA molecules to form a stable complex. Liposomesthat are pH-sensitive or negatively-charged are believed to entrap DNArather than complex with it. Both cationic and noncationic liposomeshave been used to deliver DNA to cells.

Liposomes also include “sterically stabilized” liposomes, a term which,as used herein, refers to liposomes comprising one or more specializedlipids. When incorporated into liposomes, these specialized lipidsresult in liposomes with enhanced circulation lifetimes relative toliposomes lacking such specialized lipids. Examples of stericallystabilized liposomes are those in which part of the vesicle-forminglipid portion of the liposome comprises one or more glycolipids or isderivatized with one or more hydrophilic polymers, such as apolyethylene glycol (PEG) moiety. Liposomes and their uses are furtherdescribed in U.S. Pat. No. 6,287,860.

The pharmaceutical formulations and compositions of the presentinvention may also include surfactants. The use of surfactants in drugproducts, formulations and in emulsions is well known in the art.Surfactants and their uses are further described in U.S. Pat. No.6,287,860, which is incorporated herein by reference.

In one embodiment, the present invention employs various penetrationenhancers to effect the efficient delivery of nucleic acids,particularly oligonucleotides. In addition to aiding the diffusion ofnon-lipophilic drugs across cell membranes, penetration enhancers alsoenhance the permeability of lipophilic drugs. Penetration enhancers maybe classified as belonging to one of five broad categories, i.e.,surfactants, fatty acids, bile salts, chelating agents, andnon-chelating nonsurfactants. Penetration enhancers and their uses arefurther described in U.S. Pat No. 6,287,860, which is incorporatedherein by reference.

One of skill in the art will recognize that formulations are routinelydesigned according to their intended use, i.e. route of administration.

Formulations for topical administration include those in which theoligonucleotides of the invention are in admixture with a topicaldelivery agent such as lipids, liposomes, fatty acids, fatty acidesters, steroids, chelating agents and surfactants. Lipids and liposomesinclude neutral (.g. diolcoyl-phosphatidyl DOPE ethanolamine,dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline)negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g.dioleoyltetramethylaminopropyl DOTAP and dioleoyl-phosphatidylethanolamine DOTMA).

For topical or other administration, oligonucleotides of the inventionmay be encapsulated within liposomes or may form complexes thereto, inparticular to cationic liposomes. Alternatively, oligonucleotides may becomplexed to lipids, in particular to cationic lipids. Fatty acids andesters, pharmaceutically acceptable salts thereof, and their uses arefurther described in U.S. Pat. No. 6,287,860.

Compositions and formulations for oral administration include powders orgranules, microparticulates, nanoparticulates, suspensions or solutionsin water or non-aqueous media, capsules, gel capsules, sachets, tabletsor minitablets. Thickeners, flavoring agents, diluents, emulsifiers,dispersing aids or binders may be desirable, oral formulations are thosein which oligonucleotides of the invention are administered inconjunction with one or more penetration enhancers surfactants andchelators. Surfactants include fatty acids and/or esters or saltsthereof, bile acids and/or salts thereof, bile acids/salts and fattyacids and their uses are further described in U.S. Pat. No. 6,287,860,which is incorporated herein by reference. Also are combinations ofpenetration enhancers, for example, fatty acids/salts in combinationwith bile acids/salts. A particularly combination is the sodium salt oflauric acid, capric acid and UDCA. Further penetration enhancers includepolyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether.Oligonucleotides of the invention may be delivered orally, in granularform including sprayed dried particles, or complexed to form micro ornanoparticles. Oligonucleotide complexing agents and their uses arefurther described in U.S. Pat. No. 6,287,860, which is incorporatedherein by reference.

Compositions and formulations for parenteral, intrathecal orintraventricular administration may include sterile aqueous solutionsthat may also contain buffers, diluents and other suitable additivessuch as, but not limited to, penetration enhancers, carrier compoundsand other pharmaceutically acceptable carriers or excipients.

Certain embodiments of the invention provide pharmaceutical compositionscontaining one or more oligomeric compounds in combination with one ormore additional agents. The additional agents can function by anon-antisense mechanism. A second agent is, e.g., an agent currentlyused for treatment of the Sirtuin-associated disease or disorder. Asecond agent can alternatively be a non-Sirtuin modulating agent, e.g.,a chemotherapeutic agent. For example, in the treatment of a cancer, oneor more chemotherapeutic agents useful in treating the particular cancercan be administered in combination with at least one antisenseoligonucleotide of the present invention. A combination treatmentregimen encompasses treatment regimens in which administration of a SIRTantisense oligonucleotide is initiated prior to, during, or aftertreatment with a second agent, and continues until any time duringtreatment with the second agent or after termination of treatment withthe second agent. It also includes treatments in which the agents beingused in combination are administered simultaneously or at differenttimes and/or at decreasing or increasing intervals during the treatmentperiod. Combination treatment includes periodic treatments that startand stop at various times to assist with the clinical management of thepatient. For example, an agent in the combination can be administeredweekly at the onset of treatment, decreasing to biweekly, and decreasingfurther as appropriate.

Other Sirtuin-modulating agents that can be administered to a patient incombination with the antisense oligonucleotides of the present inventionhave been described in the literature, e.g., in U.S. Pat. App. Pub. No.2000/0163476, “N-Phenyl Benzamide Derivatives as Sirtuin Modulators,”incorporated herein by reference in its entirety. This publicationreports the use of certain Sirtuin modulating compounds for treatingneurodegenerative diseases, and traumatic or mechanical injury to thecentral nervous system (CNS), spinal cord or peripheral nervous system(PNS). It also lists additional therapeutic agents that can be used incombination with Sirtuin-modulating agents. Yet other Sirtuin-modulatingagents contemplated for administration to patients in combination withthe antisense oligonucleotides of the present invention are describedin: U.S. Pat. No. 7,855,289 “Sirtuin modulating compounds” and; U.S.Pat. No. 7,829,556 “Sirtuin modulating compounds;” U.S. Pat. App. Pub.No. 2009/0143376, “Fused Heterocyclic Compounds and Their Use as SirtuinModulators;” U.S. Pat. App. Pub. No. 2009/0069301, Acridine andQuinoline Derivatives as Sirtuin Modulators;” U.S. Pat. App. Pub. No.2007/0037865, “Sirtuin modulating compounds;” U.S. Pat. App. Pub. No.2007/0149466. “Methods and related compositions for treating orpreventing obesity, insulin resistance disorders, andmitochondrial-associated disorders;” each incorporated herein byreference in its entirety.

Examples of such chemotherapeutic agents include but are not limited tocancer chemotherapeutic drugs such as daunorubicin, daunomycin,dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin,bleomycin, mafosfamide, ifosfamide, cytosine arabinoside,bischloroethyl-nitrosurea, busulfan, mitomycin C, actinomycin D,mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen,dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine,mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea,nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine,6-thioguanine, cytarabine, 5-azacytidine, hydroxyurea, deoxycoformycin,4-hydroxyperoxycyclo-phosphoramide, 5-fluorouracil (5-FU),5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol,vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan,topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol(DES). When used with the compounds of the invention, suchchemotherapeutic agents may be used individually (e.g., 5-FU andoligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for aperiod of time followed by MTX and oligonucleotide), or in combinationwith one or more other such chemotherapeutic agents (e.g., 5-FU, MTX andoligonucleotide, or 5-FU, radiotherapy and oligonucleotide).Anti-inflammatory drugs, including but not limited to nonsteroidalanti-inflammatory drugs and corticosteroids, and antiviral drugs,including but not limited to ribivirin, vidarabine, acyclovir andganciclovir, may also be combined in compositions of the invention.Combinations of antisense compounds and other non-antisense drugs arealso within the scope of this invention. Two or more combined compoundsmay be used together or sequentially.

In another related embodiment, compositions of the invention may containone or more antisense. compounds, particularly oligonucleotides,targeted to a first nucleic acid and one or more additional antisensecompounds targeted to a second nucleic acid target. For example, thefirst target may be a particular antisense sequence of a Sirtuin (SIRT),and the second target may be a region from another nucleotide sequence.Alternatively, compositions of the invention may contain two or moreantisense compounds targeted to different regions of the same Sirtuin(SIRT) nucleic acid target. Numerous examples of antisense compounds areillustrated herein and others may be selected from among suitablecompounds known in the art. Two or more combined compounds may be usedtogether or sequentially.

Dosing

The formulation of therapeutic compositions and their subsequentadministration (dosing) is believed to be within the skill of those inthe art. Dosing is dependent on severity and responsiveness of thedisease state to be treated, with the course of treatment lasting fromseveral days to several months, or until a cure is effected or adiminution of the disease state is achieved. Optimal dosing schedulescan be calculated from measurements of drug accumulation in the body ofthe patient. Persons of ordinary skill can easily determine optimumdosages, dosing methodologies and repetition rates. Optimum dosages mayvary depending on the relative potency of individual oligonucleotides,and can generally be estimated based on EC50s found to be effective inin vitro and in vivo animal models. In general dosage is from 0.01 μg to100 g per kg of body weight, and may be given once or more daily,weekly, monthly or yearly, or even once every 2 to 20 years. Persons ofordinary skill in the art can easily estimate repetition rates fordosing based on measured residence times and concentrations of the drugin bodily fluids or tissues. Following successful treatment, it may bedesirable to have the patient undergo maintenance therapy to prevent therecurrence of the disease state, wherein the oligonucleotide isadministered in maintenance doses, ranging from 0.01 μg to 100 g per kgof body weight, once or more daily, to once every 20 years.

In embodiments, a patient is treated with a dosage of drug that is atleast about 1, at least about 2, at least about 3, at least about 4, atleast about 5, at least about 6, at least about 7, at least about 8, atleast about 9, at least about 10, at least about 15, at least about 20,at least about 25, at least about 30, at least about 35, at least about40, at least about 45, at least about 50, at least about 60, at least,about 70, at least about 80, at least about 90, or at least about 100mg/kg body weight. Certain injected dosages of antisenseoligonucleotides are described, e.g., in U.S. Pat. No. 7,563,884,“Antisense modulation of PTPlB expression,” incorporated herein byreference in its entirety.

While various embodiments of the present invention have been describedabove, it should be understood that they have been presented by way ofexample only, and not limitation. Numerous changes to the disclosedembodiments can be made in accordance with the disclosure herein withoutdeparting from the spirit or scope of the invention. Thus, the breadthand scope of the present invention should not be limited by any of theabove described embodiments.

All documents mentioned herein are incorporated herein by reference. Allpublications and patent documents cited in this application areincorporated by reference for all purposes to the same extent as if eachindividual publication or patent document were so individually denoted.By their citation of various references in this document. Applicants donot admit any particular reference is “prior art” to their invention.Embodiments of inventive compositions and methods are illustrated in thefollowing examples.

EXAMPLES

The following non-limiting Examples serve to illustrate selectedembodiments of the invention. It will be appreciated that variations inproportions and alternatives in elements of the components shown will beapparent to those skilled in the art and are within the scope ofembodiments of the present invention.

Example 1 Design of Antisense Oligonucleotides Specific for a NucleicAcid Molecule Antisense to a Sirtuin (SIRT) And/or a Sense Sound of aSirtuin (SIRT) Polynucleotide

As indicated above the term, “oligonucleotide specific for” or“oligonucleotide targets” refers to an oligonucleotide having a sequence(i) capable of forming a stable complex with a portion of the targetedgene, or (ii) capable of forming a stable duplex with a portion of anmRNA transcript of the targeted gene.

Selection of appropriate oligonucleotides is facilitated by usingcomputer programs that automatically align nucleic acid sequences andindicate regions of identity or homology. Such programs are used tocompare nucleic acid sequences obtained, for example, by searchingdatabases such as GenBank or by sequencing PCR products. Comparison ofnucleic acid sequences from a range of species allows the selection ofnucleic acid sequences that display an appropriate degree of identitybetween species. In the case of genes that have not been sequenced,Southern blots are performed to allow a determination of the degree ofidentity between genes in target species and other species. Byperforming Southern blots at varying degrees of stringency, as is wellknown in the art, it is possible to obtain an approximate measure ofidentity. These procedures allow the selection of oligonucleotides thatexhibit a high degree of complementarity to target nucleic acidsequences in a subject to be controlled and a lower degree ofcomplementarity to corresponding nucleic acid sequences in otherspecies. One skilled in the art will realize that there is considerablelatitude in selecting appropriate regions of genes for use in thepresent invention.

An antisense compound is “specifically hybridizable” when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a modulation of function and/oractivity, and there is a sufficient degree of complementarity to avoidnon-specific binding of the antisense compound to non-target nucleicacid, sequences under conditions in which specific binding is desired,i.e., under physiological conditions in the case of in vivo assays ortherapeutic treatment, and under conditions in which assays areperformed in the case of in vitro assays.

The hybridization properties of the oligonucleotides described hereincan be determined by one or more in vitro assays as known in the art.for example, the properties of the oligonucleotides described herein canbe obtained by determination of binding strength between the targetnatural antisense and a potential drug molecules using melting curveassay.

The binding strength between the target natural antisense and apotential drug molecule (Molecule) can be estimated using any of theestablished methods of measuring the strength of intermolecolarinteractions, for example, a melting curve assay.

Melting curve assay determines the temperature at which a rapidtransition from double-stranded to single-stranded conformation occursfor the natural antisense/Moleoule complex. This temperature is widelyaccepted as a reliable measure of the interaction strength between thetwo molecules.

A melting curve assay can be performed using a cDNA copy of Ac actualnatural antisense RNA molecule or a synthetic DNA or RNA nucleotidecorresponding to the binding site of the Molecule. Multiple kitscontaining all necessary reagents to perform this assay are available(e.g. Applied Biosystems inc. MeltDoctor kit). These kits include asuitable buffer solution containing one of the double strand DNA (dsDNA)binding dyes (such as ABI HRM dyes, SYBR Green, SYTO, etc.). Theproperties of the dsDNA dyes are such that they emit almost nofluorescence in free form, but are highly fluorescent when bound todsDNA.

To perform the assay the cDNA or a corresponding oligonucleotide aremixed with Molecule in concentrations defined by the particularmanufacturer's protocols. The mixture is heated to 95° C. to dissociateall pre-formed dsDNA complexes, then slowly cooled to room temperatureor other lower temperature defined by the kit manufacturer to allow theDNA molecules to anneal. The newly formed complexes are then slowlyheated to 95° C. with simultaneous continuous collection of data on theamount of fluorescence that is produced by the reaction. Thefluorescence intensity is inversely proportional to the amounts of dsDNApresent in the reaction. The data can be collected using a real time PCRinstrument compatible with the kit (e.g. ABI's StepOne Plus Real TimePCR System or LightTyper instrument, Roche Diagnostics, Lewes, UK).

Melting peaks are constructed by plotting the negative derivative offluorescence with respect to temperature (-d(Fluorescence)/dT) on they-axis) against temperature (x-axis) using appropriate software (forexample LightTyper (Roche) or SDS Dissociation Curve, ABI). The data isanalyzed to identity the temperature of the rapid transition from dsDNAcomplex to single strand molecules. This temperature is called Tm and isdirectly proportional to the strength of interaction between the twomolecules. Typically, Tm will exceed 40° C.

Example 2 Modulation of SIRT Polynucleotides Treatment of HepG2 Cellswith Antisense Oligonucleotides

HepG2 cells from ATCC (cat#HB-8065) were grown in growth media (MEM/EBSS(Hyclone cat#SH30024, or Mediatech cat #MT-10-010-CV)+10% FBS (Mediatechcat#MT35-011-CV)+ penicillin/streptomycin (Mediatech cat#MT30-002-Cl))at 37° C. and 5% CO₂. One day before the experiment the cells werereplated at the density of 1.5×10⁵/ml into 6 well plates and incubatedat 37° C. and 5% CO₂. On the day of the experiment the media in the 6well plates was changed to fresh growth media. All antisenseoligonucleotides were diluted to the concentration of 20 μM. Two μl ofthis solution was incubated with 400 μl of Opti-MEM media (Gibcocat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogen cat#11668019)at room temperature for 20 min and applied to each well of the 6 wellplates with HepG2 cells. A Similar mixture including 2 μl of waferinstead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO₂ the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega(cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181)following the manufacturers' instructions. 600 ng of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) or High Capacity cDNA ReverseTranscription Kit (cat#4368813) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman GeneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay: Hs00202021_ml. Hs00202030_ml,Hs00953479_(—ml, Hs)00202033_ml, Hs00978329_ml, Hs00213036_ml andHs00213029_ml by Applied Biosystems Inc. Foster City Calif.). Thefollowing PCR cycle was used: 50° C. for 2 min, 95° C. for 10 min, 40cycles of (95° C. for 15 seconds, 60° C. for 1 min) using StepOne PlusReal Time PCR Machine (Applied Biosystems). Fold change in geneexpression after treatment with antisense oligonucleotides wascalculated based on the difference in 18S-normalized dCt values betweentreated and mock-transfected samples.

Results

Real time PCR results show that the levels of the SIRT1 mRNA in HepG2cells significantly increased 48 h after treatment with some antisenseoligonucleotides to SIRT1 antisense CV396200 (FIGS. 3,4).

Real Time PCR results show that levels of SIRT1 mRNA in HepG2 cells aresignificantly increased in one of the oligonucleotides designed to SIRT1antisense CV396200 (FIG. 8).

Real Time PCR results show that levels of SIRT1 mRNA in HepG2 cells aresignificantly increased in two of the oligonucleotides designed to SIRT1antisense CV428275 (FIG. 9).

The results show that a significant increase in SIRT1 mRNA levels inHepG2 cells 48 hours after treatment with one of the oligonucleotidesdesigned to SIRT antisense BE717453. (FIG. 10).

The results show that show that the levels of the SIRT1 mRNA in HepG2cells are significantly increased 48 h after treatment with three of theoligonucleotides designed to SIRT1 antisense AV718812 respectively (FIG.11).

Real time PCR results show that the levels of SIRT1 mRNA in HepG2 cellsare significantly increased 48 h after treatment with two of the oligosdesigned to SIRT1 antisense AW169958 (FIG. 12).

RT PCR results show that sirt3 levels in HepG2 cells are increased 48hours after treatment with phosphorothioate antisense oligonucleotidesdesigned to sirt3 antisense Hs.683117 (CUR-1545-1550) (FIG. 17).

RT PCR results show that sirt3 levels in HepG2 cells are increased 48hours after treatment with phosphorothioate antisense oligonucleotidesdesigned to sirt3 antisense BQ024738 and BE164357 (FIG. 18).

RT PCR results show that sirt3 levels in HepG2 cells are increased 48hours after treatment with siRNA oligonucleotides designed to sirt3antisense RIC8A and PMSD13 (FIG. 19)

Real Time PCR results show that levels of SIRT4 mRNA in HepG2 cells aresignificantly increased 48 h after treatment with one of the antisenseoligonucleotides to SIRT4 antisense (FIG. 22).

Real Time PCR results show that levels of SIRT5 mRNA in HepG2 cells aresignificantly increased 48 h after treatment with one of the antisenseoligonucleotides to SIRT5 antisense Hs.671550 (FIG. 23).

Real time PCR results show that the levels of SIRT6 mRNA in HepG2 cellsare significantly increased 48 h after treatment with one of the oligosdesigned to SIRT6 antisense NM_(—)133475 (FIG. 24).

Real time PCR results show that the levels of SIRT6 mRNA in HepG2 cellsare significantly increased 48 h after treatment with one of the oligosdesigned to SIRT6 antisense bf772662 (FIG. 25).

Real time PCR results show that the levels of SIRT7 mRNA in HepG2 cellsare significantly increased 48 h after treatment with one of the oligosdesigned to SIRT7 antisense (FIG. 29).

Treatment of 3T3 Cells with Antisense Oligonucleotides

3T3 cells from ATCC (cat#CRL-1658) were grown in growth media (MEM/EBSS(Hyclone cat#SH30024, or Mediatech cat#MT-10-010-CV) +10% FBS (Mediatechcat#MT35-011-CV)+ penicillin/streptomycin (Mediatech cat#MT30-002-Cl))at 37° C. and 5% CO₂. One day before the experiment the cells werereplated at the density of 1.5×10⁵/ml into 6 well plates and incubatedat 37° C. and 5% CO₂. On the day of the experiment the media in the 6well plates was changed to fresh growth media. All antisenseoligonucleotides were diluted to the concentration of 20 μM. Two μl ofthis solution was incubated with 400 μl of Opti-MEM media (Gibcocat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogen cat#11668019)at room temperature for 20 min and applied to each well of the 6 wellplates with 3T3 cells. A Similar mixture including 2 μl of water insteadof the oligonucleotide solution was used for the mock-transfectedcontrols. After 3-18 h of incubation at 37° C. and 5% CO₂ the media waschanged to fresh growth media. 48 h after addition of antisenseoligonucleotides the media was removed and RNA was extracted from thecells using SV Total RNA Isolation System from Promega (cat#Z3105) orRNeasy Total RNA Isolation kit from Qiagen (cat#74181) following themanufacturers' instructions. 600 ng of RNA was added to the reversetranscription reaction performed using Verso cDNA kit from ThermoScientific (cat#AB1453B) or High Capacity cDNA Reverse Transcription Kit(cat#4368813) as described in the manufacturer's protocol. The cDNA fromthis reverse transcription reaction was used to monitor gene expressionby real time PCR rising ABI Taqman Gene Expression Mix (cat#4369510) andprimers/probes designed by ABI (Applied Biosystems Taqman GeneExpression Assay; Hs00202021_ml by Applied Biosystems Inc., Foster CityCalif.). The following PCR cycle was used: 50° C. for 2 min, 95° C. for10 min, 40 cycles of (95° C. for 15 seconds. 60° C. for 1 min) usingStepOne Plus Real Time PCR Machine (Applied Biosystems). Fold change ingene expression after treatment with antisense oligonucleotides wascalculated based on the difference in 18S-normalized dCt values betweentreated and mock-transfected samples.

Results

Real time PCR results show that the levels of SIRT1mRNA aresignificantly increased in 3T3 cells 48 h after treatment with three ofthe oligonucleotides designed to SIRT1mouse antisense AK044604 (FIG.13).

Real time PCR results show that the levels of SIRT1 mRNA aresignificantly increased in 3T3 cells 48 h after treatment with five ofthe oligonucleotides designed to SIRT1mouse antisense AK044604 (FIG.14).

Real time PCR results show that the levels of SIRT1mRNA aresignificantly increased in 3T3 cells 48 h after treatment with two ofthe oligonucleotides designed to SIRT1mouse antisense AK044604 (FIG.15).

Real time PCR results show that the levels of SIRT1mRNA aresignificantly increased in 3T3 cells 48 h after treatment with two ofthe oligonucleotides designed to SIRT1mouse antisense AK044604 (FIG.16).

Treatment of Vero76 Cells with Antisense Oligonucleotides

Vero76 cells from ATCC (cat#CRL-1587) were grown in growth media(MEM/EBSS (Hyclone cat#SH30024, or Mediatech cat#MT-10-10-010-CV)+10%FBS (Mediatech cat#MT35-011-CV)+ penicillin/streptomycin (Mediatechcat#MT30-002-Cl)) at 37° C. and 5% CO2. One day before the experimentthe cells were replated at the density of 1.5×10⁵/ml into 6 well platesand incubated at 37° C. and 5% CO2. On the day of the experiment themedia in the 6 well plates was changed to fresh growth media. Allantisense oligonucleotides were diluted in water to the concentration of20 μM. 2 μl of this solution was incubated with 400 μl of Opti-MEM media(Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogencat#11668019) at room temperature for 20 min and applied to each well ofthe 6 well plates with Vero76 cells. Similar mixture including 2 μl ofwater instead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO2 the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega(cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181),following the Manufacturers' instructions. 600 ng of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman GeneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay: Hs00202021_ml by AppliedBiosystems Inc., Foster City Calif.). The following PCR cycle was used:50° C. for 2 min, 95° C. for 10 min, 40 cycles of (95° C. for 15seconds, 60° C. for 1 min) using StepOne Plus Real Time PCR Machine(Applied Biosystems). Fold change in gene expression after treatmentwith antisense oligonucleotides was calculated based on the differencein 18S-normalized dCt values between treated and mock-transfectedsamples.

Results

Real time PCR results show that the levels of the SIRT1mRNA in Verocells significantly increased 48 h after treatment with antisenseoligonucleotides to SIRT1antisense CV396200 (FIG. 5).

Real time PCR results show that the levels of the SIRT3 mRNA in Verocells significantly increased 48 h after treatment with antisenseoligonucleotides to SIRT3 antisense PSMD13 (FIG. 20). Real Time PCRresults show that levels of SIRT7 mRNA in Vero76 cells are significantlyincreased 48 h after treatment with one of the antisenseoligonucleotides to SIRT7 antisense CA308253 (FIG. 27).

Treatment of HUVEC Cells with Antisense Oligonucleotides

HUVEC cells from ATCC (Promo Cell cat#C-12253) were grown in EpithelialGrowth Media (Promo Cell cat#C-22010) at 37° C. and 5% CO2. One daybefore the experiment the cells were replated using Promo Cell DetachKit (cat#C-41200) at the density of 1.5×10⁵/ml into 6 well plates andincubated at 37° C. and 5% CO2. On the day of the experiment the mediain the 6 well plates was changed to fresh Epithelial Growth Media. Allantisense oligonucleotides were diluted to the concentration of 20 μM.Two μl of this solution was incubated with 400 μl of Opti-MEM media(Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogencat#11668019) at room temperature for 20 min and applied to each well ofthe 6 well plates with HUVEC cells. Similar mixture including 2 μl ofwater instead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO2 the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega(cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181)following the manufacturers' instructions. 600 ng of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman geneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay: Hs00202033_ml by AppliedBiosystems Inc., Foster City Calif.). The following PCR cycle was used:50° C. for 2 min, 95° C. for 10 min, 40 cycles of (95° C. for 15seconds, 60° C. for 1 min) using StepOne Plus Real Time PCR Machine(Applied Biosystems Inc.) or Mx4000 thermal cycler (Stratagene). Foldchange in gene expression after treatment with antisenseoligonucleotides was calculated based on the difference in18S-normalized dCt values between treated and mock-transfected samples.

Results: Real Time PCR results show that levels of SIRT4 mRNA in HUVECcells are significantly increased 48 h after treatment with one of theantisense oligonucleotides to SIRT4 antisense AA 156947 (FIG. 21).

Treatment of DBS Cells with Antisense Oligonucleotides

DBS cells from ATCC (cat#CCL-161) were grown in growth media (MEM/EBSS(Hyclone cat#SSH30024, or Mediatech cat#MT-010-010-CV)+10% FBS(Mediatech cat#MT35-011-CV)+ penicillin/streptomycin (Mediatechcat#MT30-002-Cl)) at 37° C. and 5% CO₂. One day before the experimentthe cells were replated at the density of 1.5×10⁵/ml into 6 well platesand incubated at 37° C. and 5% CO₂. On the day of the experiment themedia in the 6 well plates was changed to fresh growth media. Allantisense oligonucleotides were diluted to the concentration of 20 μM.Two μl of this solution was incubated with 400 μl of Opti-MEM media(Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogencat#11668019) at room temperature for 20 min and applied to each well ofthe 6 well plates with 3T3 cells. A Similar mixture including 2 μl ofwater instead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO₂ the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega(cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181)following the manufacturers' instructions. 600 ng of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) or High Capacity cDNA ReverseTranscription Kit (cat#4368813) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman GeneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay; Hs00202021_ml Hs00202030_ml,Ms00202033_ml, Hs00978329_ml, Hs00213036_ml and Hs00213029_ml by AppliedBiosystems Inc., Foster City Calif.). The following PCR cycle was used:50° C. for 2 min, 95° C. for 10 min, 40 cycles of (95° C. for 15seconds, 60° C. for 1 min) using StepOne Plus Real Time PCR Machine(Applied Biosystems). Fold change in gene expression after treatmentwith antisense oligonucleotides was calculated based on the differencein 18S-normalized dCt values between treated and mock-transfectedsamples.

Results: Real time PCR results show that the levels of SIRT6 mRNA in DBScells are significantly increased 48 h after treatment with two of theoligo designed to SIRT6 antisense bf772662 and one oligo designed toNM_(—)133475 (FIG. 26).

Treatment of SK-N-AS Cells with Antisense Oligonucleotides

SK-N-AS cells (neuroblastoma ATCC#CRL-2137) were grown in DMEM(Mediatech cat#10-013-CV)+10% FBS (Mediatechcat#MT35-011-CV)+penicillin/streptomycin (Mediatech cat#MT30-002-CI) at37° C. and 5% CO2. One day before the experiment the cells were replatedat the density of approximately 3×10⁵/well into 6 well plates andincubated at 37° C. and 5% CO2 overnight. At dosing the cells were about75% confluent. To dose, the media in the 6 well plates was changed tofresh DMEM+10% FBS+penicillin+streptomycin (1.5 ml/well). All antisenseoligonucleotides were diluted to the concentration of 20 uM inDNAse/RNAse-free sterile water (working stock). To dose one well, 2 ulof this solution was incubated with 400 ul of Opti-MEM media (Gibcocat#31985-070) and 4 ul of Lipofectamine 2000 (Invitrogen cat#11668019)at room temperature for 20 min, then applied dropwise to one well of a 6well plate with SK-N-AS cells (final oligo concentration=20 nM). Aninactive oligonucleotide at the same concentration was used as control.Additionally one well on each plate was dosed with a mixture of 400 ulof Opti-MEM media, 4 ul of Lipofectamine 2000 and 2 ul ofDNAse/RNAse-free sterile water was for the mock-transfected controls.After about 18 h of incubation at 37° C. and 5% CO2 the media waschanged to fresh DMEM+10% FBS+penicillin+streptomycin. Approximately 48h after addition of antisense oligonuclotides the media was removed andRNA was extracted from the cells using SV Total RNA Isolation Systemfrom Promega (cat#Z3105) following the manufacturers' instructions. 600ng of RNA was added to the reverse transcription reaction performedusing High Capacity cDNA kit from Applied Biosystems (cat#4368813) asdescribed in the manufacturer's protocol. The cDNA from this reversetranscription reaction was used to monitor gene expression by real timePCR using ABI Taqman Gene Expression Mix (cat#4369510) andprimers/probes designed by ABI (assay ID#Hs00213029_ml for SIRT7). Thefollowing PCR cycle was used: 50° C. for 2 min, 95° C. for 10 min, 40cycles of (95° C. for 15 seconds, 60 ° C. for 1 min) on the StepOne PlusReal Time PCR system (Applied Biosystems). The assay for 18S wasmanufactured by ABI (cat#4319413E). Fold change in gene expression aftertreatment with antisense oligonuclotides was calculated based on thedifference in 18S-normalized dCt values between treated andmock-transfected samples.

Results: Real time PCR results show that the levels of SIRT7 mRNA inSK-N-AS cells are significantly increased 48 h after treatment witholigos designed to SIRT7 antisense (FIG. 28).

Example 3 Modulation of SIRT Gene Expression Materials and MethodsTreatment of HepG2 Cells with Naked Antisense Oligonucleotides

HepG2 cells from ATCC (cat#HB-8065) were grown in growth media (MEM/EBSS(Hyclone cat#SH30024, or Mediatech cat#MT-10-010-CV)+10% FBS (Mediatechcat#MT35-011-CV)+penicillin/streptomycin (Mediatech cat#MT30-002-Cl)) at37° C. and 5% CO2. One day before the experiment the cells were replatedat the density of 0.5×10⁵/ml into 6 well plates and incubated at 37° C.and 5% CO2. On the day of the experiment the media in the 6 well plateswas replaced with 1.5 ml/well of fresh growth media. All antisenseoligonucleotides were diluted in water to the concentration of 20 μM. 2μl of this solution was incubated with 400 μl of Opti-MEM media (Gibcocat#31985-070) and 4 ul of Lipofectamine 2000 (Invitrogen cat#11668019)at room temperature for 20 min and applied to each well of the 6 wellplates with HepG2 cells. Similar mixture including 2 μl of water insteadof the oligonucleotide solution was used for the mock-transfectedcontrols. After 3-18 h of incubation at 37° C. and 5% CO2 the media waschanged to fresh growth media. 72 h after addition of antisenseoligonucleotides the cells were redosed as described above, 48 h afterthe second dosing of antisense oligonucleotides the media was removedand RNA was extracted from the cells using SV Total RNA Isolation Systemfrom Promega (cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen(cat#74181) following the manufacturers' instructions. 600 ng of RNA wasadded to the reverse transcription reaction performed using Verso cDNAkit from Thermo Scientific (cat#AB1453B) as described in themanufacturer's protocol. The cDNA from this reverse transcriptionreaction was used to monitor gene expression by real time PCR using ABITaqman Gene Expression Mix (cat#4369510) and primers/probes designed byABI (Applied Biosystems Taqman Gene Expression Assay: Hs00202021_ml,Hs00202030_ml, Hs00202033_ml, Hs00978329_ml, Hs00213036_ml andHs00213029_ml by Applied Biosystems Inc., Foster City Calif.). Thefollowing PCR cycle was used: 50° C. for 2 min, 95° C. for 10 min, 40cycles of (95° C. for 15 seconds, 60° C. for 1 min) using StepOne PlusReal Time PCR Machine (Applied Biosystems). Fold change in geneexpression after treatment with antisense oligonucleotides wascalculated based on the difference in 18S-normalized dCt values betweentreated and mock-transfected samples.

Primers and probe for the custom designed Taqman assay for exon 4;

(SEQ ID NO: 128) AACTGGAGCTGGGGTGTCTGTTTCAthe SIRT1 natural antisense CV396200. Forward Primer Seq.(SEQ ID NO: 129) CCATCAGACGACATCCCTTAACAAA Reverse Primer Seq.(SEQ ID NO: 130) ACATTATATCATAGCTCCTAAAGGAGATGCA Reporter Seq.(SEQ ID NO: 131) CAGAGTTTCAATTCCCResults: The results show that the levels of the SIRT1mRNA in HepG2cells are significantly increased 48 h after treatment with one of thesiRNAs designed to sirtas (sirtas_(—)5, P=0.01). In the same samples thelevels of sirtas RNA were significantly decreased after treatment withsirtas_(—)5, but unchanged after treatment with sirtas_(—)6 andsirtas_(—)7, which also had no effect on the SIRT1mRNA levels (FIG. 2).sirtas_(—)5, sirtas_(—)6 and sirtas_(—)7 SEQ ID NOs: 47.48 and 49respectively.

Treatment of Primary Monkey Hepatocytes

Primary monkey hepatocytes were introduced into culture by RxGen Inc.and plated in 6 well plates. They were treated with oligonucleotides asfollows. The media in the 6 well plates was changed to fresh growthmedia consisting of William's Medium E (Sigma cat#W4128) supplementedwith 5% FBS, 50 U/ml penicillin and 50 ug/ml streptomycin, 4 ug/mlinsulin, 1 uM dexamethasone, 10 ug/ml Fungin (InVivogen, San DiegoCalif.). All antisense oligonucleotides were diluted to theconcentration of 20 μM, 2 μl of this solution was incubated with 400 μlof Opti-MEM media (Gibco cat#1985-070) and 4 μl of Lipofectamine 2000(Invitrogen cat#11668019) at room temperature for 20 min and applied toeach well of the 6 well plates with cells. Similar mixture including 2μl of water instead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO2 the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega(cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181)following the manufacturers' instructions. 600 ug of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman GeneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay: Hs00202021_ml, Hs00202030_ml,Hs00202033_ml, Hs00978329_ml, Hs00213036_ml and Hs00213029_ml by AppliedBiosystems Inc., Foster City Calif.). The following PCR cycle was used:50° C. for 2 min, 95° C. or 10 min, 40 cycles of (95° C. for 15 seconds,60° C. for 1 min) using Mx4000 thermal cycler (Stratagene). Fold changein gene expression after treatment with antisense oligonucleotides wascalculated based on the difference in 18S-normalized dCt values betweentreated and mock-transfected samples.

Results: The results are shown in FIG. 7. Real time PCR results show anincrease in SIRT1 mRNA levels after treatment with an oligonucleotideagainst SIRT1 antisense.

Example 4 Efficacy and Duration of Action Study of CUR 963 in theAfrican Green Monkey

The objective of this study was to assess and compare the effect ofantisense knockdown of the discordant noncoding antisense sequences thatregulate the SIRT1 genes following intravenous administration in anonhuman primate model. The antisense oligonucleotide test articlesdesigned to inhibit the SIRT1 regulatory sequences were designated asCUR 963.

CUR 963: (SEQ ID NO: 43) +G*+T*C*T*G*A*T*G*G*+A*+G*+A.CUR 962 (control): (SEQ ID NO: 132) +G*+C*T*A*G*T*C*T*G*+T*+T*+G.

Regulatory Test Guidelines

This study was designed in accordance with accepted toxicologicalprinciples and to comply with International Conference of Harmonization(ICH) Harmonized Tripartite Guidelines (Non-Clinical Safety Studies forthe Conduct of Human Clinical Trials for Pharmaceuticals ICH M3(m), 2000Nov. 9), and generally accepted procedures for the testing oftherapeutic agents.

Test And Control Articles Test Article Identity and Preparation

The test article, CUR-963, is a chemically stabilized antisenseoligonucleotide. The vehicle for intravenous delivery isphosphate-buffered saline (PBS).

Vehicle Characterization

For the PBS vehicle, the composition, batch number, expiry date andstorage conditions (temperature and Light/dark) was obtained from thesupplier.

Test Article Storage and Handling

The test substance and vehicle were stored according to the receivedstorage conditions supplied by the Sponsor and manufacturer,accordingly.

Analysis of the Test Article Formulations

Samples of the test article formulation will be cryopreserved foranalysis of the concentration, stability and homogeneity of the testsubstance formulations.

Test System Rationale

The primate is a suitable non rodent species, acceptable to regulatoryauthorities as an indicator of potential hazards, and for whichextensive background data are available. The African green monkeyspecifically is a highly clinically relevant model of multiple humanphysiologic and disease states.

The intravenous route of administration corresponds to a possible humantherapeutic route. The dose of the test articles was based on theresults of the dose finding studies of analogous compounds previouslyperformed in the African green monkey.

African green monkeys were chosen as the primate of choice as the testsubstances' target sequences are conserved across species with 100%homology in primates. Additionally, the test substance is a syntheticoligonucleotide. Consequently, dosing in primates allows for a superiorassessment of the efficacy of these compounds that would be morereflective of the uptake likely to be seen in humans than in any otherspecies.

Animals

Species Chorocebus sabaeus, non-human primate

Breed: African green monkey indigenous to St. Kitts.

Source: RxGen, Lower Bourryeau, Si, Kitts, West Indies.

Expected Age: The test animals were adults.

Expected Body Weight: The monkeys weigh approximately 3-4 kg. The actualrange may vary but will be documented in the data.

Sex: The test animals were adult females.

Number of Animals: Ten animals were screened to ensure identification of8 animals appropriate for enrollment in the study.

Number on Study: Females: 8

Justification for Number on Study: This study was designed to use thefewest number of animals possible, consistent with the primary objectiveof evaluating the therapeutic efficacy of the test article in theAfrican green monkey and prior studies of the systemic administration ofthis type of oligonucleotide in this Species.

Animal Specification: Ten adult African Green monkeys in the weightrange of 3 to 4 kg, were employed in the study. The monkeys weredrug-naïve adult animals humanely trapped from the feral population thatinhabits the island. Trapped monkeys were treated with antihelminthicsto eliminate any possible intestinal parasite burden and were observedin quarantine for a minimum of 4 weeks prior to screening for studyenrollment. The age of trapped monkeys were estimated by size anddentation, with the exclusion of older animals from the study. Prior tostudy enrollment, a clinical exam was performed on each monkey,including evaluation of locomotion and dexterity. Blood samples weretaken and sent to Antech Diagnostics (Memphis, Tenn.) for comprehensiveclinical chemistries and a complete blood count and lipid profiles (seesections 9.2 and 319507928 for specifications). Monkeys with abnormallab values, as determined by comparison to the established normal rangefor monkeys in the St. Kitts colony, were excluded from the study. Inorder to identify 8 monkeys that satisfy this criterion, 10 monkeys werescreened, with the screening of additional animals as needed. Beforestudy initiation, the selected monkeys will be transferred to individualcages to acclimate to individual housing for a one-week period. Onlyanimals deemed suitable for experimentation will be enrolled in thestudy. The actual (or estimated) age and weight ranges at the start ofthe study will be detailed in the raw data and final report.

Animals Health and Welfare: The highest standards of animal welfare werefollowed and adhered to guidelines stipulated by the St. KittsDepartment of Agriculture and the U.S. Department of Health and HumanServices. All studies will be conducted in accordance with theserequirements and all applicable codes of practice for the care andhousing of laboratory animals. All applicable standards for veterinarycare, operation, and review as contained in the NIH Guide for the Careand Use of Animals. The St. Kitts facility maintains an animal researchcommittee that reviews the protocols and inspects the facilities asrequired by the Guide. The Foundation has an approved assurance filedwith the Office of Laboratory Animal Welfare, as required by the Guide,#A4384-01 (Axion Research Foundation/St. Kitts Biomedical Foundation).There are no special nonhuman primate veterinary care issues andbiohazard issues raised by the research specified in this study.

Housing and Environment: To allow detection of any treatment-relatedclinical signs, the animals were housed individually prior to surgeryand postoperatively until sacrifice. The primate building in which theindividual cages were situated were illuminated entirely by ambientlight, which at 17 degrees north latitude approximates a 12 hr:12 hrlight-dark cycle as recommended in the U.S. D.H.H.S guidelines. TheRxGen primate building was completely ventilated to the outside.Additional air movement was assured by ceiling fans to maintain aconstant target temperature of 23-35° C., as is typical of St. Kittsthroughout the year. Twenty-four hour extremes of temperature andrelative humidity (which also will not be controlled) were measureddaily. During the study, the cages were cleaned at regular intervals,

Diet and Water: Bach animal was offered approximately 90 grams per dayof a standard monkey chow diet (TekLad, Madison, Wis.). The specificnutritional composition of the diet was recorded. The water wasperiodically analyzed for microbiological purity. The criteria foracceptable levels of contaminants in stock diet and water supply werewithin the analytical specifications established by the dietmanufacturer and the periodic facility water evaluations, respectively.The water met all criteria necessary for certification as acceptable forhuman consumption.

Experimental Design

Animal Identification and Randomization: Allocation was done by means ofa stratified randomization procedure based on bodyweight and plasmacholesterol profiles. Prior to and after allocation to a group, eachanimal was identified by a tattoo on the abdomen. Tattoos are placed onall colony animals as a means of identification in the course of routinehealth inspections. A cage plan was drawn up to identify the individualshoused within, and individual monkeys were further identified by alabeled tag attached to their respective cage.

Group sizes, doses and identification numbers: The animals were assignedto 2 treatment groups, comprised of 4 monkeys in each group. Specificanimal identification numbers were provided to each monkey according tothe facility numbering system. This system uniquely identifies eachmonkey by a letter followed by a three digit number, e.g. Y032.

Route and Frequency of Administration: Animals were dosed once daily onDays 1, 3, and 5 delivered intravenously by manual infusion over-10 min.The infusion rate will be 24 mL/kg/h. The animals were sedated withketamine and xylazinc prior to and during the dosing procedure. A venouscatheter (Terumo mini vein infusion set, 20 gauge needle, or similarappropriate infusion set) was inserted into the saphenous vein. Dosingtook place in each monkey between 8:00 and 10:00 a.m. shortly after theanimals wake and prior to feeding. A blood sample to assess plasmacholesterol and other lipid levels as described in Blood Chemistrysection below, was collected just prior to each infusion. Bloodcollection preceded feeding at both sampling intervals to minimizedietary effects on cholesterol measurements.

Clinical Observations: All visible signs of reaction to treatment wererecorded on each day of dosing. In addition, the animals were examinedat least once each week for physical attributes such as appearance andgeneral condition.

Body Weights: Body weights were recorded at weekly intervals during thetreatment and post-treatment periods.

Food Consumption: Individual food consumption was not quantified.Feeding patterns were however monitored and a note made of any majorchanges.

Mortality and Morbidity: Mortality and morbidity will be recorded. Anydecision regarding premature sacrifice will be made after consultationwith the Study Director and wish the Sponsor's Monitoring Scientist, ifpossible. Animals that are found dead or killed prematurely will besubjected to necropsy with collection of liver, kidney, heart and spleenlung tissues for histopathology. In the event of premature sacrifice ablood sample will also be taken (if possible) and the parametersdetermined. Animals that are found dead after regular working hours willbe refrigerated overnight and necropsies performed at the start of thenext working day. If the condition of an animal requires prematuresacrifice, it will be euthanized by intravenous overdose of sodiumpentobarbital. All research is governed by the Principles for Use ofAnimals. RxGen is required by law to comply with the U.S. Department ofHealth and Human Services standards for primate facility, which dictatesthe levels of severity that the procedures within this study, specifiedas mild, must abide.

Clinical Laboratory Studies

Fat Biopsies: A subcutaneous fat biopsy was performed on all studymonkeys except Y775 on study days 26 by tissue extraction through a 1 cmmidline incision inferior to the umbilicus. Biopsies were immediatelyimmersed in a labeled cryotube containing 2 mls of RNAlater (Qiagen) andincubated at 4° C. overnight, after which the RNAlater was aspirated andthe sample tube flash frozen in liquid nitrogen. Followingtransportation in liquid nitrogen total RNA was isolated for real-timeqPCR of target genes.

Results. Real time PCR results show an increase in SIRT1mRNA levels infat biopsies from monkeys dosed with CUR-963, an oligonucleotidedesigned to SIRT1 antisense CV396200.1, compared to monkeys dosed withCUR-962 (SEQ ID NO.: 132), an oligonucleotide which had no effect onSIRT1 expression in vivo (designed to ApoA1 antisense DA327409, data notshown). mRNA levels were determined by real time PCR (FIG. 6).

Example 5 In vivo Modulation of Sirtuin (SIRT) by Antisense DNAOligonucleotides

Treatment with Antisense DNA Oligonucleotides (ASO); Antisenseoligonucleotides (ASO) specific for SIRT1 AS are administered toC57Bl/6J mice which are fed a high fat diet for 12 weeks to induceobesity and diabetes. The treatment of the mice with ASO will start atthe time of the implementation of the high fat diet. Mice are injectedIP once a week with ASO prepared in normal saline, at a concentration of5 mg/kg.

Measurements of body weight and food intake: Body weight and food intakeof mice are measured twice per week, prior to IP injection of the ASO.

Blood glucose measurements: Fed and fasted blood glucose concentrationsare measured each week by taking a sample of blood from the tail vein.

Glucose Tolerance Tests (GTT): The GTT will be done totally twice permouse, halfway through the diet (at week 4) and near the end (at week10) of the high fat diet. The GTT will inform us about the glucosetolerance of the mice that is the capacity to rapidly clear a glucosebolus from the blood stream. This is a measure for diabetes. Mice arefasted overnight for 16 hours. Mice are injected IP glucose 2 g/kg. Thistranslates into a final volume of 0.2 ml 30% (w/v) glucose solution fora mouse of 30 g weight. Glucose measurements are taken prior to glucoseinjection and at 5, 15, 30, 60, 90 and 120 min post-injection. Glucoseis measured by cutting the tail tip 1 mm from the end of the tail underisoflurane anesthesia prior to IP glucose injection. The blood dropletis aspirated into a strip and glucose concentration is measured with aglucometer. The GTT will be done totally twice per mouse, halfwaythrough the diet (at week 4) and near the end (at week 10) of the highfat diet. The GTT will inform us about the glucose tolerance of the micethat is the capacity to rapidly clear a glucose bolus from the bloodstream. This is a measure for diabetes.

Insulin Tolerance Test (ITT): Mice are fasted for 6 hours from 9 am till3 pm. Mice are then injected IP 0.5-1U Insulin/kg. The insulinconcentration will be adjusted such that the final injected volume is0.1-0.15 ml. Blood, glucose measurements are taken prior to injectionand at 5, 15, 30,45, and 60 minutes post-injection. Blood is collectedexactly as described under GTT. In addition to monitoring the glucoselevels, the behavior of the mice is constantly observed during the ITT.Hypoglycemia can manifest as a change in behavior with the animalsbecoming very quiet and showing discomfort. To prevent hypoglycemia,glucose (1 g/kg) is injected IP in a final volume of 0.1 -0.15 ml assoon as the blood glucose concentration falls below 50 mg/ml or signs ofdiscomfort are observed.

Blood Collection by Facial Vein Puncture: Mice are restrained by thescruff of the neck and base of the tail, slightly compressing the bloodvessels of the neck through the tautness of the grip on the neck skin.The sampling site is on the jaw slightly in front of the angle of themandible. The skin at the sampling site is punctured with an 18 G needleor a lancet at a 90° angle until the tip of the needle/lancer justpasses through the skin. Blood samples are collected usingmicrohematocrit tubes. After blood has been collected, the grip on theneck is loosened and pressure is applied at the insertion site with agauze sponge to ensure hemostasis. 0.05-0.2ml of blood will be collectedby this method. This procedure will be performed only once in week 5 ofthe high fat diet and eventually in week 12 if the intracardiac punctureis not working (see below). Blood hormones which regulate the metabolismof glucose and lipids (such as insulin, adiponectin and leptin) aremeasured using commercially available ELISA kits. (e.g., R&D Systems,Minneapolis, Minn., Assay Pro St. Charles, Mo., Mabtech, Mariemont,Ohio)

Intracardiac Puncture: At the end of the 12 week high fat diet, micewill be anesthetized by continuous isoflurane inhalation. Anesthesia isinduced by placing the mice in an induction box, which is supplied withisoflurane and oxygen. Mice will be restrained on their back. The heartis punctured with a 27 G needle. Following exsanguineation, the head isdecapitated to ensure death. Tissues (liver, pancreas, white and brownadipose tissue, and skeletal muscle) are collected for furtherinvestigations (RNA and protein measurements and histology). Around0.5-1 ml of blood will be obtained and used to determine severalcritical parameters of glucose and lipid metabolism (glucose, insulin,cholesterol, triglycerides, free fatty acids, leptin, adipokines,corticosteroids, thyroid hormones). If difficulties occur in thismethod, we will collect blood by facial vein puncture under isofluraneanesthesia instead (see above).

Although the invention has been illustrated and described with respectto one or more implementations, equivalent alterations and modificationswill occur to others skilled in the art upon the reading andunderstanding of this specification and the annexed drawings. Inaddition, while a particular feature of the invention may have beendisclosed with respect to only one of several implementations, suchfeature may be combined with one or more other features of the otherimplementations as may be desired and advantageous for any given orparticular application.

The Abstract of the disclosure will allow the reader to quicklyascertain the nature of the technical disclosure. It is submitted withthe understanding that it will not be used to interpret or limit thescope or meaning of the following claims.

What is claimed is:
 1. A method of modulating a function of and/or theexpression of a Sirtuin (SIRT) polynucleotide in patient cells ortissues in vivo or in vitro comprising: contacting said cells or tissueswith at least one antisense oligonucleotide 5 to 30 nucleotides inlength wherein said at least one oligonucleotide has at least 50%sequence identity to a reverse complement of a polynucleotide comprising5 to 30 consecutive nucleotides within nucleotides 1 to 1028 of SEQ IDNO: 9 or nucleotides 1 to 429 of SEQ ID NO: 10, or nucleotides 1 to 508of SEQ ID NO: 11 or nucleotides 1 to 593 of SEQ ID NO: 12, 1 to 373 ofSEQ ID NO: 13, 1 to 1713 of SEQ ID NO: 14, 1 to 660 of SEQ ID NO: 15, 1to 589 of SEQ ID NO: 16, 1 to 726 of SEQ ID NO: 17, 1 to 320 of SEQ IDNO: 18, 1 to 616 of SEQ ID NO: 19, 1 to 492 of SEQ ID NO: 20, 1 to 428of SEQ ID NO: 21, 1 to 4041 of SEQ ID NO: 22 or 1 to 705 of SEQ ID NO:23 or 1 to 2714 of SEQ ID NO: 141 or 1 to 1757 of SEQ ID NO: 142 or 1 to3647 of SEQ ID NO: 143; thereby modulating a function of and/or theexpression of the Sirtuin (SIRT) polynucleotide in patient cells ortissues in vivo or in vitro.
 2. (canceled)
 3. (canceled)
 4. (canceled)5. (canceled)
 6. (canceled)
 7. (canceled)
 8. (canceled)
 9. (canceled)10. (canceled)
 11. (canceled)
 12. (canceled)
 13. (canceled) 14.(canceled)
 15. (canceled)
 16. (canceled)
 17. A synthetic, modifiedoligonucleotide of 10 to 30 nucleotides in length comprising at leastone modification wherein the at least one modification is selected from:at least one modified sugar moiety; at least one modifiedinternucleotide linkage; at least one modified nucleotide, andcombinations thereof; wherein said oligonucleotide is an antisensecompound which hybridizes to a natural antisense polynucleotide of aSirtuin (SIRT) 2, 3, 4, 5 or 7 gene and upregulates the function and/orexpression of a Sirtuin (SIRT) in vivo or in vitro as compared to anormal control.
 18. The oligonucleotide of claim 17, wherein the atleast one modification comprises an internucleotide linkage selectedfrom the group consisting of: phosphorothioate, alkylphosphonate,phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate,carbonate, phosphate triester, acetamidate, carboxymethyl ester, andcombinations thereof.
 19. The oligonucleotide of claim 17, wherein saidoligonucleotide comprises at least one phosphorothioateinternucleotide-linkage.
 20. The oligonucleotide of claim 17, whereinsaid oligonucleotide comprises a backbone of phosphorothioateinternucleotide linkages.
 21. The oligonucleotide of any of claims17-20, wherein the oligonucleotide comprises at least one modifiednucleotide, said modified nucleotide selected from: a peptide nucleicacid, a locked nucleic acid (LNA), analogue, derivative, and acombination thereof.
 22. The oligonucleotide of any of claims 17-21,wherein the oligonucleotide comprises a plurality of modifications,wherein said modifications comprise modified nucleotides selected from:phosphorothioate, alkylphosphonate, phosphorodithioate,alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphatetriester, acetamidate, carboxymethyl ester, and a combination thereof.23. The oligonucleotide of any of claims 17-22, wherein theoligonucleotide comprises a plurality of modifications, wherein saidmodifications comprise modified nucleotides selected from: peptidenucleic acids, locked nucleic acids (LNA), analogues, derivatives, and acombination thereof.
 24. The oligonucleotide of any of claims 17-23,wherein the oligonucleotide comprises at least one modified sugar moietyselected from: a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxymodified sugar moiety, a 2′-O-alkyl modified sugar moiety, a bicyclicsugar moiety, and a combination thereof.
 25. The oligonucleotide of anyof claims 17-24, wherein, the oligonucleotide comprises a plurality ofmodifications, wherein said modifications comprise modified sugarmoieties selected from: a 2′-O-methoxyethyl modified sugar moiety, a2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, abicyclic sugar moiety, and a combination thereof.
 26. (canceled) 27.(canceled)
 28. (canceled)
 29. The oligonucleotide of any of claims17-28, wherein the oligonucleotide comprises at least one of thesequences set form as SEQ ID NOS: 24 to
 127. 30. A compositioncomprising one or more oligonucleotides according to claim 17 and apharmaceutically acceptable excipient.
 31. The composition of claim 30,wherein the oligonucleotides have at least about 40% sequence identityas compared to any one of the nucleotide sequences set forth as SEQ IDNOS: 24 to
 127. 32. The composition of claim 30, wherein theoligonucleotides comprises any of the nucleotide sequences set forth asSEQ ID NOS: 24 to
 127. 33. The composition of claim 31 or claim 32,wherein the oligonucleotides set forth as SEQ ID NOS: 24 to 127 compriseone or more modifications or substitutions.
 34. The composition of claim33, wherein the one or more modifications are selected from:phosphorothioate, methylphosphonate, peptide nucleic acid, lockednucleic acid (LNA) molecules, and combinations thereof.
 35. A method ofpreventing or treating a disease associated with at least one Sirtuin(SIRT) polynucleotide and/or at least one encoded product thereof,comprising: administering to a patient a therapeutically effective doseof at least one antisense oligonucleotide of 10 to 30 nucleotides inlength that binds to a natural antisense sequence of said at least oneSirtuin (SIRT) polynucleotide and modulates expression of said at leastone Sirtuin (SIRT) polynucleotide; thereby preventing or treating thedisease associated with the at least one Sirtuin (SIRT) polynucleotideand/or at least one encoded product thereof.
 36. The method of claim 35,wherein a disease associated with the at least one Sirtuin (SIRT)polynucleotide is selected from: a disease or disorder associated withabnormal function and/or expression of Sirtuin, cancer (e.g., breastcancer, colorectal cancer, CCL, CML, prostate cancer), aneurodegenerative disease or disorder (e.g., Alzheimer's Disease (AD),Huntington's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis(ALS), Multiple Sclerosis, and disorders caused by polyglutamineaggregation), a beta-amyloid disease or disorder (e.g., a disordercharacterized by .beta.-amyloid accumulation such as Alzheimer'sdisease), skeletal muscle disease (e.g., Duchene muscular dystrophy,skeletal muscle atrophy, Becker's dystrophy, or myotonic dystrophy); ametabolic disease or disorder (e.g., insulin resistance, diabetes, type2 diabetes, obesity, impaired glucose tolerance, metabolic syndrome,adult-onset diabetes, diabetic nephropathy, hyperglycemia, diabeticnephropathy, Hypercholesterolemia, dyslipidemia hyperlipidemia and anage-related metabolic disease etc.), a disease or disorder associatedwith impaired insulin regulation, neuropathy (e.g., sensory neuropathy,autonomic neuropathy, motor neuropathy, retinopathy), a disease ordisorder associated with a ketogenic condition, a disease or disorderassociated with impaired energy homeostasis, a disease or disorderassociated with impaired Acetyl-CoA synthetase 2 activity, a disease ordisorder associated with metabolic homeostasis, a lipid metabolismdisease or disorder, a disease or disorder associated with impairedthermogenesis, a disease or disorder associated with impaired regulationof cell division, a disease or disorder associated with mitochondrialdysfunction, neuropathy (e.g., sensory neuropathy, autonomic neuropathy,motor neuropathy, retinopathy), fibrosis, inflammatory cardiomyopathy,heart hypertrophy, Ichronic inflammation, atherosclerosis, arthritis,dementia, osteoporosis, and a cardiovascular disease or disorder, ahepatic disease or disorder (e.g., due to alcohol abuse or hepatitis,fatty liver disease etc.), age-related macular degeneration, bonedisease (e.g., osteoporosis), a blood disease (e.g., a leukemia), boneresorption, age-related macular degeneration, AIDS related dementia,ALS, Bell's Palsy, atherosclerosis, a cardiac disease or disorder (e.g.,cardiac dysrhymias, chronic congestive heart failure, ischemic stroke,coronary artery disease and cardiomyopathy), chronically degenerativedisease (e.g., cardiac muscle disease), chronic renal failure, type 2diabetes, ulceration, cataract, presbiopia, glomerulonephritis,Gullian-Barre syndrome, hemorrhagic stroke, rheumatoid arthritis,inflammatory bowel disease, SLE, Crohn's disease, osteoarthritis,osteoporosis, Chronic Obstructive Pulmonary Disease (COPD), pneumonia,skin aging, a skin disease or disorder, urinary incontinence, a diseaseor disorder associated with mitochondrial dysfunction (e.g.,mitochondrial myopathy, encephalopathy, Leber's disease, Leighencephalopathia, Pearson's disease, lactic acidosis, ‘mitochondrialencephalopathy, lactic acidosis and stroke like symptoms’ (MELAS) etc.),liver degeneration, skeletal muscle degeneration, a muscular disease ordisorder, inflammation, a disease or disorder associated with ectopiclipid storage, a disease or disorder associated with oxidative stress, adisease or disorder associated with cellular stress, a disease ordisorder associated with neuronal cell death, aging or other conditioncharacterized by unwanted cell loss, degenerative syndrome, a disease ordisorder associated with ammonia detoxification, aging, a disease ordisorder associated with telomere dysfunction, a disease or disorderassociated with impaired chromatin regulation, a disease or disorderassociated with premature cellular senescence, a disease or disorderassociated with impared SIRT mediated DNA repair and a conditioncharacterized by unwanted cell loss.
 37. A method of preventing ortreating a skin condition associated with at least one Sirtuin (SIRT)polynucleotide and/or at least one encoded product thereof, comprising;administering to a patient having a skin condition or at risk ofdeveloping a skin condition a therapeutically effective dose of at leastone antisense oligonucleotide that binds to a natural antisense sequenceof said at least one Sirtuin (SIRT) polynucleotide and modulatesexpression of said at least one Sirtuin (SIRT) polynucleotide; therebypreventing or treating the disease skin condition associated with the atleast one Sirtuin (SIRT) polynucleotide and/or at least one encodedproduct thereof.
 38. The method of claim 38, wherein the skin conditionis caused by caused by inflammation, light damage or aging.
 39. Themethod of claim 38 or claim 39, wherein the skin condition is thedevelopment of wrinkles, contact dermatitis, atopic dermatitis, actinickeratosis, ketatinization disorders, an epidermolysis bullosa disease,exfoliative dermatitis, seborrheic dermatitis, an erythema, discoidlupus erythematosus, dermatomyositis, skin cancer, or an effect ofnatural aging. A method according to any of claims 1-16 or 35-39,wherein, modulation of a Sirtuin is determined by assaying for theSirtuin or a Sirtuin biomarker.
 40. The method of claim 39, wherein aSirtuin biomarker selected from the group consisting of MCP-1, BMPReceptor 1A, Smpd13a, CD14, ApoE, FAS, Transthyretin, FABP1, Acyl-CoAthioesterase 1, Acyl-CoA thioesterase 2, Aquaporin 4, Rrad, CXCL9, CCL8,Ppplr3g, ApoA-I, ApoA-II, and ApoB is assayed.